But Comey administered an extraordinary tongue-lashing to Clinton and her aides, rebuking them for being "extremely careless" in the handling of classified information and saying the presumptive Democratic nominee should have known an unclassified email system was no place to conduct sensitive government business.
The FBI director pointed out that the probe was tasked with examining whether Clinton or her aides had mishandled classified information either intentionally or in a grossly negligent way.
"Our judgment is that no reasonable prosecutor would bring such a case," Comey announced after a lengthy recap of the investigation apparently designed to protect the integrity of his agency in a highly charged political atmosphere.
Comey's decision not to recommend charges likely removes the threat of prosecution in the middle of Clinton's campaign for the presidency, but the political fallout will continue. His explicit criticism of Clinton's conduct offered her enemies a trove of fresh ammunition for their assault on her character, honesty and trustworthiness — one of her biggest vulnerabilities.
In a stunning moment of Washington theater, Comey stepped up to the microphone to deliver the FBI's findings just over two hours before Clinton climbed aboard Air Force One to travel to her first campaign event with President Barack Obama. Adding to the tension, he made clear the White House and the Justice Department "do not know what I am about to say."
White House Press Secretary Josh Earnest said the White House doesn't have an official response to the FBI's announcement, saying the case is still active and in the hands of the Department of Justice.
Earnest added: "I am confident that the President and Secretary Clinton are not discussing the FBI investigation that is completed" on Air Force One. Neither Obama nor Clinton addressed Comey's remarks during their campaign event in Charlotte, North Carolina, though Obama praised Clinton's work at the State Department.
Comey delivered a stern lecture to Clinton and State Department colleagues at her side during her tenure as top U.S. diplomat between 2009 and 2013.
"Although we did not find clear evidence that Secretary Clinton or her colleagues intended to violate laws governing the handling of classified information," he said, "there is evidence that they were extremely careless in their handling of very sensitive, highly classified information."
In the first reaction from the Clinton camp to Comey's statement, spokesman Brian Fallon said that the campaign was "pleased that the career officials handling this case have determined that no further action by the Department is appropriate.
"As the secretary has long said, it was a mistake to use her personal email and she would not do it again. We are glad that this matter is now resolved."
Later, aides said they were relieved by the announcement, even though they know it's far from being in their rearview mirror.
The findings of the FBI probe immediately detonated on the campaign trail with presumptive Republican nominee Donald Trump crying foul.
"The system is rigged. ... Very very unfair! As usual, bad judgment," Trump tweeted
. He later issued a statement in which he claimed U.S. "adversaries almost certainly have a blackmail file on Hillary Clinton," which he said "disqualifies" her from the presidency.
At a Tuesday evening rally in North Carolina, Trump again pointed to the FBI's decision as fresh evidence of a "rigged system."
"Whats going on is very big ... for Bill Clinton to go to the plane, then to have what happened ... Everybody thought based on what was being said she was guilty. She was guilty. And it turned out that, 'We're not going to press charges.' It's really amazing," Trump said as his crowd of supporters broke out in a chorus of boos.
And House Speaker Paul Ryan said Comey's announcement "defies explanation."
"No one should be above the law," Ryan said in a statement. "But based upon the director's own statement, it appears damage is being done to the rule of law. Declining to prosecute Secretary Clinton for recklessly mishandling and transmitting national security information will set a terrible precedent."
Ryan later recommended on Fox News' Kelly File that the Director of National Intelligence "should block her access to classified information" as a form of punishment. And he said House Republicans would ask Comey to answer them in hearings on Capitol Hill.
"There are a lot of unanswered questions here," Ryan said, though he did would not say that Comey folded to political pressure when asked. "He shredded the case that she had been making all year long."
Republican National Committee Chairman Reince Priebus blasted the FBI's decision.
"I certainly don't understand how you describe a textbook definition of gross negligence, and you have case after case after case of soldiers and other military personnel being kicked out of the military ... for things that are far less egregious than what Hillary Clinton did," Priebus told CNN's Wolf Blitzer on "The Situation Room."
"First of all, it's not going to go away," he said. "I think in many ways this is going to be even worse for Hillary Clinton."
He said watching Comey's news conference, he expected criminal charges against Clinton, and called his decision "a real head-scratcher."
"Hillary Clinton lied about something that was very basic," Priebus said.
But CNN senior political commentator David Axelrod, who formerly worked for Obama, said that Tuesday's dramatic developments were the "best result" Clinton could have hoped for.
"As a political matter, what Hillary Clinton needed was a resolution -- and she got it today," Axelrod said on CNN.
Clinton has admitted her use of a private email server — discovered during investigation by the House Select Committee — on Benghazi was a mistake. But she has maintained that she never received or passed on information that was marked classified at the time -- a legalistic position that has exposed her to significant political fire.
Comey said that the FBI "painstakingly" combed through every bit of Clinton's multiple servers and mobile devices that they could from her four-year tenure as secretary of state. He described a series of obstacles, including a server that had its software wiped.
"It was like removing the frame from a huge jigsaw puzzle and then dumping all the pieces on the floor. ... We searched through all of it," he said.
The Justice Department is considered highly likely to accept Comey's recommendations. Attorney General Loretta Lynch said as much amid a furor last week over her encounter with former President Bill Clinton on an airport tarmac in Phoenix, which sparked claims by Republicans that a fix was being concocted to ensure Hillary Clinton was not charged.
Comey said of the 30,000 emails that Clinton's team turned over to the State Department, 110 emails in 52 email chains were determined to have contained classified information "at the time they were sent or received," Comey said. Eight of those chains contained information considered "top secret," the highest level of classification.
That's in addition to 2,000 emails that were "upclassified," or determined to have classified information only in hindsight.
Comey also said the FBI found "thousands" of emails that were work-related but deleted and not given to the State Department, either by regular purging by Clinton or officials during her tenure or mistaken deletion by her lawyers removing personal emails before turning over work-related emails to the State Department.
Three of those were classified at the time, he said.
However, Comey said there was not evidence of any kind of coverup in regards to those emails.
"We believe our investigation has been sufficient to give us reasonable confidence that there was no intentional misconduct in relation to that sorting effort," Comey said.
He also noted that while the FBI could find no direct evidence of an intrusion into Clinton's server by hostile foreign governments, given that she corresponded with individuals whose accounts were compromised and that the server was not secured by government protections, and that she used her email in hostile foreign territories, "It is possible that hostile actors gained access to Secretary Clinton's email account."
Ultimately, Comey said his recommendation against charges stems from the fact that there is no precedent for charging someone under similar circumstances, saying the FBI could not find a single case in which a person was charged with crimes for similar actions.
"Although there is evidence of potential violations of the statutes regarding the handling of classified information, our judgment is that no reasonable prosecutor would bring such a case," Comey said, saying the FBI could not find a single case in which a person was charged with crimes for similar actions.
He also emphatically stated that the investigation was conducted fairly and unbiased.
"This investigation was done honestly, competently and independently. No outside influence of any kind was brought to bear," Comey said. "Opinions are irrelevant. ... We did our investigation the right way. Only facts matter, and the FBI found them here in an entirely apolitical and professional way."