Scutaro opened the game's scoring with a first-inning sacrifice fly. After the Diamondbacks tied it on Jason Kubel's solo homer in the bottom of the frame, Scutaro delivered a two-run double in the third to provide the decisive blow.
Wilin Rosario added a bases-empty home run in the fourth for Colorado, which avoided a three-game sweep at the hands of the Diamondbacks.
Jeff Francis (3-2) collected the victory, holding Arizona to two runs on five hits while walking one and fanning four in six innings.
Diamondbacks starter Trevor Cahill (8-9) was touched for four runs on eight hits in a 6 2/3-inning effort as Arizona saw its five-game winning streak snapped.
Miguel Montero went 3-for-3 with a solo homer in the loss.