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.