"I'm happy to have the procedure behind me," Baker said in statement released by the team. "I look forward to getting back on the field with my teammates as soon as possible."
The Falcons released no details on the procedure and have not announced a timetable for Baker's return.
Baker, a first-round pick from USC, has started five games but was held out of last week's game against the Philadelphia Eagles with what was called a hip injury.
Baker was examined by specialists who found a problem in his lower back.
Baker had a discectomy, a surgery to remove herniated disc material that presses on a nerve root or the spinal cord, according to WebMD.com.
Baker also missed the Sept. 28 game at Carolina with a concussion after leaving two games earlier in the month with head injuries.
Falcons coach Mike Smith said Todd Weiner, who started for Baker at Philadelphia last week before leaving with a sore knee, should start at left tackle on Sunday at Oakland. Weiner didn't practice on Wednesday and had limited participation on Thursday.
The Falcons signed free-agent tackle Wayne Gandy on Wednesday.