Lewis did not accompany the team to Atlanta on Sunday, and his agent last week asked the team to release him.
Coach Mike Singletary said Monday that he told Lewis last week, either Monday or Tuesday, that there might be some changes on defense. He said he finally decided to make a change on Friday.
Lewis left the team and, according to his agent, Rodney Williams, did not intend to return. At the time, Williams said, "The relationship is beyond repair."
Asked if he felt Lewis was not playing up to standards, Singletary said, "The bottom line is, we felt that we needed to make a change. That's all it was."
Since joining the 49ers as a free agent in 2007, Lewis, 30, played in 50 games, all starts. Earlier this summer, he took a pay cut from $4.1 million to $1.7 million, plus a $400,000 roster bonus, to play one final season with the team. The Niners, however, wanted to ease Mays into the lineup, and it was Lewis who would see reduced playing time.
In a statement released by the 49ers, Singletary said: "I want to thank Michael for his hard work and leadership as a 49er. We wish him and his family all the best."