Cubs shortstop Starlin Castro was pulled shortly after making a mental mistake that let the Cardinals score in the fifth.
The Cardinals led 1-0 and had the bases loaded with one out when Castro caught a popup by Matt Carpenter in short left field. Castro put his head down and hesitated to throw home, looking as if he thought the inning was over. Jon Jay scored from third base and the other runners advanced.
Cubs manager Dale Sveum said something to Castro when he reached the dugout. Donnie Murphy switched from third base to shortstop to replace Castro in the sixth, and Cody Ransom came off the bench to play third.
Kelly (4-3) hasn't lost since joining the Cardinals rotation on July 6. He allowed four hits, struck out six and walked three.
A trio of St. Louis relievers combined to allow one hit. Both teams finished with five hits.
The Cubs have lost 14 of their last 19 game. They have been shut out in five of their last seven at Wrigley Field.
Molina homered off Travis Wood (7-10) for a 4-0 lead in the sixth after Matt Holliday was hit by a pitch. Molina's ninth homer was his first hit in eight at-bats since he came off the disabled list Thursday.
Wood retired the first nine St. Louis batters. He gave up four runs and four hits in 5 1-3 innings.
Carpenter hit a leadoff double in the fourth and scored on a double by Carlos Beltran for a 1-0 lead.
NOTES: The Cardinals recalled LHP Tyler Lyons from Triple-A Memphis before the game. He is 2-4 with a 5.35 ERA in seven starts. LHP Sam Freeman was optioned to Memphis after pitching four scoreless innings Friday against the Cubs. ... Cubs OF Brian Bogusevic, on the 15-day disabled list since July 15 for a strained left hamstring, will report to Triple-A Iowa to continue rehab. ... Cubs RHP Scott Baker, on the 60-day disabled list recovering from Tommy John surgery, will make his second rehab start Sunday with Single-A Dayton. ... Cubs RHP Edwin Jackson (7-12, 5.05 ERA) will face Cardinals RHP Adam Wainwright (13-7, 2.71) Sunday in the series finale.
Link to box score: St. Louis 4 at Chicago 0
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Tom Verducci and Rich Waltz break down the Cardinals' 4-0 win over the Cubs.