Peralta (6-9) worked around four walks and struck out six en route to his first shutout in 24 career starts for Milwaukee. The Dominican right-hander tossed 71-of-113 pitches for strikes in the gem.
The Brewers had gone a major league-worst 407 games since their last shutout, which came in April 2011.
Logan Schafer provided the game's only runs with his first big-league homer, a two-run shot in the fifth.
Reds starter Tony Cingrani (3-1) took the loss despite yielding just the two runs on three hits over seven innings.
Cincinnati fell for the fourth time in five games with the defeat.
McPhee, Cokas 'working on their marriage' after affair
LGBT community has 'bullied the American people': Bachmann