Molina left the game in the second inning with a strained right oblique and will be reevaluated on Thursday.
"It wasn't that bad, but I didn't want to make it worse," Molina said. "I don't know how long it will take to recover. Hopefully it's only a couple of days."
Molina injured his oblique while sliding into second on a double. He advanced to third on David Freese's single to center but did not try to score. He left the game immediately thereafter, walking off the infield holding his right side.
The loss of Molina concerned manager Tony La Russa, who only hours before was eagerly anticipating Pujols' return to lineup.
Pujols, the reigning National League MVP, was scratched from Monday's lineup before undergoing an MRI and receiving an anti-inflammatory injection. He followed Tuesday's off day by going 0 for 3 with a walk.
The same injury caused Pujols to miss a week earlier this spring, but the first baseman doesn't expect the injury to linger into the season.
"I can't see the future, but I'm not concerned about it," Pujols said. "My goal is to be ready for opening day and I think I will be there. I'm not worried about anything."
Injuries aside, La Russa had hoped to use Wednesday's game to judge the performance of two pitchers vying to be the Cardinals' fifth starter.
Wednesday's starter, Rich Hill, allowed two earned runs on four hits while walking three in three innings.
"Today was a day that kind of summed up spring training -- it was a couple good innings and one bad inning," said Hill, who has allowed at least one run in all four spring starts, none of which have lasted more than three innings.
Kyle McClellan followed Hill, rebounding from his toughest outing of the spring with his best performance. The right-hander tossed three scoreless innings of two-hit ball and didn't walk anyone to improve to 2-1.
"I think Rich was better [than he's been]," La Russa said. "I think Kyle continues to pitch well. It's a healthy situation for us."
Baltimore prospect Brian Matusz delivered his longest start of the spring, allowing three earned runs on nine hits in six innings.
Freese went 3 for 4 and drove in three runs for the Cardinals.