The Phillies announced Girardi received a three-year contract with a team option in 2023. He will be introduced at a news conference Monday.
"I'm excited for this next chapter of my career," Girardi said in a statement. "The Phillies have a strong commitment to winning from the owners to the front office to the players to the fans. It's something that I've seen up close for the last 30 years of my baseball career.
"I played against the great Phillies players of the early '90s from Dutch Daulton to John Kruk to Dave Hollins, and I managed against their teams during the incredible run they had from 2008 to 2011. To have my name now associated with this great franchise is something that I couldn't be happier about."
Girardi, who will wear No. 25 with the franchise, replaces Gabe Kapler as the 55th manager in Phillies history. Kapler was fired after two disappointing seasons with the club, including an 81-81 record and a fourth-place finish in the NL East despite adding star outfielder Bryce Harper last season.
The Phillies haven't had a winning season since 2011, when the team concluded a run of five consecutive NL East titles, two pennants and one World Series championship under former manager Charlie Manuel.
"Joe brings high character and a tremendous work ethic to his position, and he is a proven winner," Phillies general manager Matt Klentak said in a statement. "I look forward to working with him and I believe that he is the right manager to lead our team to the next level."
Girardi, 55, served as the Yankees' manager from 2008 to 2017, winning a World Series title in 2009. He had a 910-710 record in that span.