The Rockies scored twice in the eighth inning to tie it and then won it in the ninth when Fowler and Rutledge unloaded against San Diego's Huston Street (0-1).
Colorado had lost three in a row and the Padres have now dropped three straight.
A fielding error by San Diego third baseman Jedd Gyorko led the way to two Colorado runs, which scored on a double by Todd Helton and a ground out from Wilin Rosario.
Rex Brothers (1-0) worked the eighth for Houston and was credited with the win. Rafael Betancourt struck out one in a perfect ninth for his fourth save.