The team fell to 5-10 Sunday, and the loss to the Rams knocks them from playoff contention in a wide-open NFC West.
A preseason favorite to win the division, San Francisco underachieved all the way, never living up to its expectations.
Defensive line coach Jim Tomsula will replace Singletary for the final game against Arizona.
Singletary went 18-22 in two-plus seasons as 49ers head coach, including a surprising 8-8 mark last year. But this season has been an almost wire-to-wire disaster.
Flip-flopping between starting quarterbacks, Singletary had a confrontation with his last choice during Sunday’s loss in St. Louis, jawing with Troy Smith on the sideline after he threw an interception.
Singletary is known, of course, as a Hall-of-Fame linebacker with the Chicago Bears. But he called coaching the 49ers one of the greatest experiences of his life.
“What made it so special were the players,” Singletary said in a release issued by the team. “They were some of the most outstanding men I have ever been around in my life.”
Singletary called the coaches “professionals” and said he wished the team “nothing but the best.” He thanked the owners for giving him an opportunity to coach in the NFL.
“I am indebted to them for that,” Singletary said. “I am also thankful for the faithful fans, I am just sorry I couldn’t give them more.”
Tomsula was in his fourth season as the 49ers defensive line coach after a nine-year career in NFL Europa.
A full-time head coach isn’t the only position the team will have to fill in the offseason. The 49ers have been working without a general manager since firing Scot McCloughan back in March.