Jonathan Lucroy's bases-clearing double chased Wainwright (13-6) in a four-run sixth inning that put Milwaukee up by six. The NL Central leaders are three games ahead of the Cardinals.
Matt Carpenter had two hits and three RBIs and Matt Holliday homered for St. Louis, which has lost three of four.
Peralta, Wainwright and the Dodgers' Clayton Kershaw all have 13 wins. Last year, the 25-year-old Peralta (13-6) was 11-15 with a 4.37 ERA in his first full season in the majors.