Molina's shot put the Giants up 3-0 and Jose Castillo hit a solo homer in the fourth for the eventual game-winning run. Ray Durham and Aaron Rowand also drove in runs.
Tim Lincecum (7-1) scattered three runs on six hits over 7 1/3 innings to give the Giants their fourth win in six games. Brian Wilson pitched a 1-2-3 ninth for his 15th save.
Dan Haren (5-4) gave up five runs on nine hits in six innings to absorb the loss for the Diamondbacks, who have dropped three of their last four.
Chris Young drove in one run and Chad Tracy hit a two-run double to account for Arizona's runs.
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