Also sitting was shortstop Aledmys Diaz, who aggravated a back injury and jammed his left shoulder diving for a ball Friday.
Both were available to pinch-hit and Diaz did, delivering the go-ahead run in St. Louis' 4-1 victory with a home run off Carlos Torres to lead off the seventh that gave the Cardinals a 2-1 lead.
"Since he had to come off the field, you kind of almost anticipate half of a game is not going to be enough," Cardinals manager Mike Matheny said of Fowler. "He came in today in better shape, which is encouraging. There's a good chance we get him back in there [Sunday]."
Diaz completed Friday's game, but Matheny said the shortstop has been bothered by a stiff back that spreads to his legs and limits mobility.
He tried to fight his way into the lineup but ultimately listened to the training staff and Matheny.
"It's kind of both things nagging," Matheny said. "It is the same idea [as Fowler] to get him a day. There's a good chance he could play tomorrow. What I explained to him is that he's going to be able to move correctly. If he has anything getting in the way, that position is one that you have to make sure you are on point."
Matheny would not rule out either player from returning Sunday, but the Cardinals could opt to give both three consecutive days off since the Cardinals do not play Monday before opening a three-game series with Toronto on Tuesday.
Greg Garcia started at shortstop and went 2-for-5 with two doubles in place of Diaz. With Fowler out, Randal Grichuk played center field and went 3-for-4 at the plate.
Andrew Gruman is a contributor to MLB.com based in Milwaukee.