Reyes singled home a run in the first inning and Stanton followed with a three-run bomb, putting the Marlins up 4-0 early.
Reyes made it 6-0 with a two-run triple in the next frame.
Nathan Eovaldi (4-8) collected the victory, allowing just one run on six hits through 6 2/3 innings. The right-hander overcame four walks and struck out three.
The Marlins' bullpen, however, surrendered four runs to make it close. Steve Cishek earned his ninth save despite allowing a two-run single to Tyler Colvin in the ninth.
Colorado's Tyler Chatwood (3-3) was tagged for six runs on nine hits over four full innings.
Colvin finished 3-for-5 with three RBI for the Rockies.