Wainwright's gem was his first shutout since 2010 and the second consecutive victory for the National League Central Division-leading Cards.
Wainwright (3-5) struck out nine and allowed one walk. He missed the 2011 season while recovering from Tommy John surgery.
The Padres, losers of six of their last 10 games, got doubles from Andy Parrino and starting pitcher Edinson Volquez (2-4), who allowed three runs on five hits and four walks over six innings.
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