Interim manager Chris Speier said Baker will meet the Reds in St. Louis on Sunday night after their game in Pittsburgh. Cincinnati opens a three-game series against the Cardinals on Monday.
"It'll be just like he never missed a beat," said Speier, the usual bench coach.
The Reds have clinched the NL Central title and are in a race with Washington for the NL's best record. Cincinnati won six of its first 10 games without Baker.
Speier said Baker was setting the team's lineups, and he even called Sunday morning to make an adjustment to the lineup.
"Everybody has to understand that I'm just following suit here," Speier said. "It hasn't been easy to take over something when you've got the mainstay of this organization going through what he went through. It's a definite cloud over us because we're worried about him and are really, really, really happy he's going to be in St. Louis."