Cain (14-7) walked two batters and struck eight on the way to ending a three-start losing streak.
Reliever Sergio Romo yielded a run and two hits before closer Brian Wilson fanned Reed Johnson for the final out to earn his 37th save.
Eli Whiteside led San Francisco with two RBI doubles. Eugenio Velez, Pablo Sandoval and Juan Uribe all had two hits and one RBI for the Giants, who maintained their slim playoff hopes, having won just three of nine.
The Giants trail the Colorado Rockies by five games in the NL wild-card chase.
Chicago's run scored on a ninth-inning triple by Bobby Scales. Four others had one hit for the Cubs, who were trying for a rare four-game sweep at San Francisco.
The losing pitcher was starter Randy Wells (11-10).
Copyright 2009 by United Press International.
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