Wells (1-1), who hadn't pitched a major league game since 2009 when he made his Padres debut Tuesday, scattered six hits, worked around a pair of walks and struck out two en route to the victory.
Luke Gregerson contributed a scoreless eighth and Huston Street collected his 12th save for the Padres, who clinched their three-game series at Coors Field.
Chris Denorfia went 2-for-5, scoring San Diego's first run on a third-inning throwing error by Rockies third baseman Jordan Pacheco and singling in Alexi Amarista in the seventh.
Colorado's Drew Pomeranz (0-3) was saddled with the hard-luck loss, yielding only one earned run on two hits over six full frames.
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