The Padres surrendered five runs in the bottom of the seventh, but still won for the third time in the four-game series.
Carlos Quentin drove in three runs, two of them with a third-inning homer, and the Padres struck for four runs in the seventh to pad their lead.
Milwaukee then sent 10 men to the plate in its half of the seventh against three San Diego pitchers and wound up stranding the potential tying runs when Will Venable made a diving catch in center on a line drive from Norichika Aoki that ended the inning.
Yonder Alonso helped fuel San Diego's 16-hit attack by going 2-for-5 with two RBI.
Edinson Volquez (8-8) survived 5 1/3 innings to get the win, giving up three runs on six hits with three walks. Huston Street eventually came on as the seventh Padres pitcher and struck out two in the ninth to earn his 19th save.
San Diego roughed up Yovani Gallardo (8-9) for six runs on eight hits in just 3 2/3 innings.