With Colorado trailing 2-0 in the fourth inning, Josh Rutledge led off with a single and scored when Dexter Fowler followed with a double.
Two outs later, Pachero came up and drove a pitch to left field that just cleared the fence, putting the Rockies ahead for good.
Ottavino (5-1) took over from starter Drew Pomeranz in the fifth, allowing only one hit while walking one and striking out two in three frames.
Marlins starter Josh Johnson (7-10) was the loser, surrendering three runs on seven hits over seven innings.
John Buck hit a solo homer for Miami.
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