Baca entered the plea in the downtown Los Angeles courtroom of U.S. District Court Judge Percy Anderson. Sentencing was set for May 16.
Baca's attorney, Michael Zweiback, said the former sheriff entered the plea, in part, because he has "immense respect" for the sheriff's department and did not want to continue to "distract from their mission."
"He feels badly that this has been a cloud hanging over the department," Zweiback said. "He is truly sorry that he put them through this."
He said Baca "accepts full responsibility for what he plead guilty to" and is looking forward to sentencing and moving on with his life.
Baca's appearance before Anderson came just hours after prosecutors announced his plea deal, which many observers saw as a stunning development in the ongoing criminal probe of the sheriff's department.
"Today's charge and plea agreement demonstrate that illegal behavior within the Sheriff's Department went to the very top of the organization," U.S. Attorney Eileen M. Decker said in a prepared statement. "More importantly, this case illustrates that leaders who foster and then try to hide a corrupt culture will be held accountable."
Zweiback said Baca was facing a maximum of six months in custody under the agreement. He said both he and prosecutors were bound by the deal. If the judge did not agree to such a sentence, the deal would become moot, he said.
Baca retired from the department in 2014 amid the ongoing FBI probe into alleged beatings and cover-ups within the sprawling county jail system.
Under the deal, Baca admitted that he lied to federal prosecutors and the FBI about efforts to hide a jail inmate cooperating with the federal corruption probe. Baca ordered the inmate to be isolated and put his second in command in charge of carrying out the plan, the plea agreement states.
He also lied in 2011 when he told federal authorities he did not know underlings were going to approach the FBI's lead agent on the case. Baca later acknowledged that he had been aware of the plan and had, in fact, directed sheriff's investigators to "do everything but put handcuffs" on the agent, according to prosecutors and court records.
The attempted intimidation, according to prosecutors, was part of an elaborate scheme to obstruct the criminal probe, which to date has resulted in eight deputies up to the rank of captain being convicted of federal charges.
A ninth official, former Undersheriff Paul Tanaka, once Baca's second in command, was indicted last year. He is accused of orchestrating a cover-up and has pleaded not guilty.
Tanaka's indictment raised questions among observers as to whether Baca would be charged.
H. Dean Steward, one of Tanaka's defense attorneys, said that he plans to call Baca as a witness when Tanaka goes to trial in March.
"We had planned to call Sheriff Baca as a witness, and that continues to be our plan," Steward and his co-counsel said in a joint statement. "His guilty plea changes nothing for our defense."
The Association for Los Angeles Deputy Sheriffs said Baca deserves punishment.
"The plea agreement sends a strong message that no one is above the law. There must be zero tolerance for this type of failed leadership. This by no means undermines the dedication and hard work of the more than 9,000 deputy sheriffs who put their lives on the line protecting L.A. County residents," the group said in a statement.
David Bowdich, the FBI's top agent in Los Angeles, said Baca missed an opportunity to lead when he first became aware of problems within the jails.
"One of the measures of an organizational culture is how it handles its allegations of misconduct," Bowdich said in a statement. "Mr. Baca set the wrong command climate and allowed that culture to fester, instead of fostering an environment of accountability."