Braun raised his home run total to 40 as the Brewers stayed in the hunt for National League wild card spot. Milwaukee cut its deficit in the wild card race to 2 1/2 games.
Peralta (2-0), making his third major-league start, yielded only two hits and one walk while fanning five. Sixty-nine of his 104 pitches were strikes.
John Axford picked up his 29th save as Milwaukee notched its 20th win in 26 contests.
New York's Chris Young (4-8) was saddled with the loss, allowing three runs on eight hits over 6 2/3 frames.