Freeze, 49, replaces former Liberty coach Turner Gill, who retired Monday after compiling a 47-35 record in seven seasons. Gill helped the Flames make the transition from the FCS to the FBS and went 6-6 this past season.
Football Scoop first reported Freeze's hiring.
Freeze resigned from Ole Miss in July 2017 in the wake of what the school termed "a pattern of personal misconduct inconsistent with the standards we expect from the leader of our football team."
At the time of Freeze's resignation, Rebels athletic director Ross Bjork told ESPN that school officials found a pattern that included phone calls to a number associated with a female escort service.
Bjork separately told ESPN that once university officials dived deeper into Freeze's phone records on a university-provided cellphone, going back as far as shortly after he was hired in 2012, they started finding more of a pattern with phone calls of the nature USA Today had earlier reported after an open-records request.
"Once we looked at the rest of the phone records, we found a pattern," Bjork told ESPN. "It was troubling."
Freeze had discussions with Auburn, Tennessee and Florida State about their vacant offensive coordinator positions in recent weeks. Alabama coach Nick Saban sought to hire him last year, but the SEC office wouldn't allow it.
Freeze and his wife, Jill, spoke about his personal misconduct during a convocation speech to the Liberty University student body in January.
"I had to say to people that I loved, 'I am sorry. Please forgive me,'" Freeze said during the school's chapel service. "And today is really the first day I can tell the faith family, 'I am sorry. Please forgive me.'"
Former Baylor athletic director Ian McCaw, who resigned in wake of the school's sexual assault scandal, is Liberty's athletic director.
Freeze had a 39-25 record in six seasons with the Rebels, including a 19-21 mark against SEC opponents. After inheriting a team that won two games in 2011 and had lost 14 consecutive SEC contests, Freeze guided the Rebels to four straight bowl games in his first four years — the first Ole Miss coach to do so. Ole Miss was one of only five FBS programs in the country to make consecutive New Year's Six bowl appearances in the first two years of the College Football Playoff.
Freeze guided the Rebels to unprecedented heights, but his success was also sullied by an NCAA investigation. In February 2017, the school self-imposed a one-year bowl ban for the 2017 season after it received a new NCAA notice of allegations that accused the school of lack of institutional control and Freeze of failure to monitor his coaching staff. In December 2017, the NCAA added additional penalties, including a bowl ban for the 2018 season, scholarship reductions and a two-game suspension for Freeze if he was hired somewhere else for the 2017 or 2018 seasons. The school was placed on probation for three years and had to vacate records of all regular-season and postseason wins in which ineligible student-athletes competed. Ole Miss also had to pay a financial penalty.
Among other charges, the NCAA accused the Rebels of providing improper benefits, including cash payments and merchandise, to prospects, as well as lodging and meals to recruits and their families.