Molina grounded out and flied out in his two at-bats before being replaced by Rob Johnson for the bottom of the fifth inning. The Reds led 6-2.
Molina missed 14 games with a strained right knee. He was activated off the disabled list Aug. 15 and had started 15 games, with manager Mike Matheny going easy on him to prevent a recurrence of the knee problem.
The Cardinals also were missing right fielder Carlos Beltran for the start of the four-game series. Beltran missed his second straight game because of a stiff back. Matheny held him out as a precaution.
St. Louis and Pittsburgh were tied for the NL Central lead.