Jonathan Lucroy, Ryan Braun and Khris Davis added run-scoring hits for NL Central Division-leading Milwaukee.
Peralta (12-6) labored through 5 2/3 innings, giving up six hits and two runs. He walked three batters and struck out two.
Peralta threw 103 pitches and didn't show the command he had in his previous outing on Monday against Cincinnati, when he surrendered three hits and one run in seven innings.
Four relievers held the Mets scoreless over the final 3 1/3 innings Saturday. Francisco Rodriguez, who blew a save and took the loss against the Mets on Friday night, recorded his 30th save in 34 chances.
Curtis Granderson had a home run and a double for the Mets. Chris Young added two doubles and reached base three times.
Jonathon Niese (5-6) took the loss, giving up five hits and three runs in five innings. He walked two batters and struck out four.
The Mets took a 1-0 lead when Granderson, mired in an 0-for-18 slump, led off the third with a double to center. He moved to third on a groundout and scored on Lucas Duda's soft single to center.
In his next at-bat, leading off the fifth, Granderson hit a line drive home run down the right-field line to make it 2-0.
The Brewers got on the board in the fifth when Jean Segura reached on a fielder's choice, stole second, advanced to third on a fly out by Peralta and scored on a wild pitch by Niese.
Milwaukee grabbed the lead later in the inning when Lucroy blasted a double to deep center with two outs, scoring Carlos Gomez, who had singled. Braun followed with an RBI single to give the Brewers a 3-2 edge.
Reynolds extended Milwaukee's lead to two runs in the sixth with a 420-foot home run to center off Carlos Torres.
The Brewers made it 5-2 in the eighth on Khris Davis' RBI double.
NOTES: The Mets placed RHP Daisuke Matsuzaka on the 15-day DL with right elbow inflammation. Matsuzaka returned to New York on Friday for an MRI. The team recalled pitcher Buddy Carlyle from Triple-A Las Vegas. ... The Brewers honored Negro League players Ted Toles Jr. and Nathan "Sonny" Weston during a pregame ceremony. ... Niese batted eighth despite entering the game with an .036 batting average. Outfielder Eric Young Jr. batted ninth. ... Milwaukee's Jimmy Nelson (1-1) faces New York's Jacob deGrom (4-5) in the series finale on Sunday.