Aoki's RBI double in the second inning put the Brewers up 3-0 and he later scored on a throwing error by Cards starting pitcher Joe Kelly.
Wily Peralta (11-15) went five innings to earn the win, allowing three runs on five hits. He overcame five walks and struck out three.
Jim Henderson notched his 26th save despite yielding three hits and a run in the ninth as the Brewers avoided a three-game sweep.
Kelly (9-5) surrendered six runs (three earned) on seven hits over seven innings for the National League Central-leading Cards, who clinched a playoff berth earlier Sunday when Washington lost to Miami.
Matt Carpenter went 2-for-3 with a solo homer for St. Louis.