Will Svitek, who started for Baker in the Falcons' 23-16 victory at Detroit two weeks ago, is expected to take his place again Sunday when Atlanta (4-3) visits Indianapolis (0-8).
Baker, a late first-round draft pick in 2008, has started 41 of 44 career games.
Early in his rookie season, Baker had surgery to repair a herniated disk.
Rookie receiver Julio Jones, the No. 6 overall pick in the draft, has practiced twice this week after missing two games with a strained left hamstring. His participation was limited on Wednesday.
Tight end Tony Gonzalez did not practice because of a sore back, but he is expected to play Sunday.