The Rockies had grabbed a 3-2 lead in the eighth on Jordan Pacheco's two-run double against David Hernandez.
But the D-backs came back in their final at-bat against Colorado closer Rafael Betancourt (1-4).
That brought up Hill, who pounded a pitch into the left-field bleachers for a walk-off, three-run shot.
Brad Ziegler (6-1) was credited with the win for Arizona, which evened its three-game season-ending series.
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