With Hill at-bat and runners on second and third, the Padres employed a five-man infield. Hill lined a shot over the head of left fielder Yonder Alonzo for his eighth career game-ending hit.
The Diamondbacks played their 20th extra-inning game this season, second only to the 21 they had in 1999. Arizona is 15-5 in this season's long contests.
San Diego dropped to 7-6 in extra innings.
Heath Bell (5-2) pitched a perfect 10th inning for the win.