"If I win, I am going to instruct my attorney general to get a special prosecutor to look into your (missing email) situation," Trump said, "because there has never been so many lies, so much deception."
Trump's threat -- which he has made before on the campaign trail
-- is extraordinary even by the standard of the vitriolic 2016 campaign.
Clinton responded first by calling Trump's comments about her emails false, then said, "It's just awfully good that someone with the temperament of Donald Trump is not in charge of the law in our country."
After the debate, Clinton campaign chairman John Podesta dismissed the remark, telling CNN's Brianna Keilar that Trump would never get the chance to follow through.
"Fortunately, he's not in charge of the laws of the country and never will be," Podesta said.
Asked about the remarks, Trump campaign chief Kellyanne Conway said the candidate was taking his cues from angry supporters.
"Donald Trump is channeling the frustration of a lot of Americans he hears from," Conway said, adding that the anger stems from what some voters perceive to be "different set of rules for this woman, as goes her emails."
Conway further elaborated in an interview on NBC's "Today" show the morning after the debate. "It was a quip," she said of Trump's threat that Clinton would be in jail if he were president. "I saw in NBC's reporting it was called a quip, so I'll go with NBC on it."
Trump's campaign manager also repeated her assertion that Trump's call for another investigation of Clinton reflected voters' frustration. "As for the special prosecutor, I think that's Donald Trump channeling the frustration he hears from thousands of voters on the stump every day. They're very frustrated that she has a different set of rules for her."
Earlier in the evening on Sunday, former White House Press Secretary Ari Fleischer, a Republican who worked for President George W. Bush, criticized Trump.
"Winning candidates don't threaten to put opponents in jail," he tweeted. "Presidents don't threaten prosecution of individuals. Trump is wrong on this."
But the sharpest attack came from former Attorney General Eric Holder, who compared Trump's threat to actions taken by President Richard Nixon at the height of the Watergate scandal.
"So @realDonaldTrump will ORDER his AG to take certain actions," Holder tweeted. "When Nixon tried that his AG courageously resigned. Trump is dangerous/unfit."
Holder was referencing one of the darkest episodes of the Nixon presidency. In what is now commonly referred to as the "Saturday Night Massacre,"
Nixon ordered his attorney general, Elliot Richardson, to fire the special prosecutor investigating the Watergate burglary.
Richardson resigned rather than follow the President's request. When Deputy Attorney General William Ruckelshaus was asked to do the same, he too refused and left the administration. Nixon ended up outsourcing the deed to Robert Bork, who formally fired special prosecutor Archibald Cox.
News broke on the morning of Sunday, October 21, 1973. Less than a year later, on August 9, 1974, Nixon resigned in disgrace.