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.
Google buys drone maker Titan Aerospace
Pistorius testifies he didn't consciously pull trigger when he shot girlfriend