Tommy Medica and Chris Robinson also hit home runs for the Padres, who piled on 10 runs in their last four at-bats.
The game was deadlocked at 2-2 in the fifth when Chris Denorfia delivered a two-run double. Gyorko added a two-run blast later in the inning.
San Diego also scored four runs in the eighth, during which Robinson contributed a three-run shot. Medica's solo homer came in the fourth and lifted the Padres into a tie.
Ian Kennedy (7-10) limited Arizona to two runs on six hits in seven innings to get the win. Randall Delgado (5-7) was roughed up for six runs on seven hits in five frames.