Immediately after the game, Peralta headed home to the Dominican Republic to take care of some ''family business,'' manager Ron Roenicke said. The pitcher will rejoin the team in Milwaukee this weekend.
Roenicke said the plan has been in place for a while. The Brewers didn't want to reveal specifics, but it sounded as though Peralta was dealing with something serious.
''Pretty tough. I don't know how he did it, but he did it. Pretty amazing, considering,'' Lucroy said. ''I don't think I could do that with stuff like that on my mind.''
Lucroy doubled twice and drove in a run, raising his batting average to .341. Carlos Gomez and Jean Segura each had an RBI as the NL Central leaders wore down Jacob deGrom (0-3), still looking for his first career win after six mostly solid starts.
The shaggy-haired rookie was lifted in the sixth after throwing 80 strikes in 107 pitches. But he got little help from his teammates as New York lost for the seventh time in eight games.
''One of these days we are going to get that big hit for him and he'll get that win,'' Mets manager Terry Collins said.
Collins made it halfway through the latest defeat, ejected in the fifth for arguing a replay ruling. The attendance of 20,170 marked the smallest crowd at Citi Field this season - for the second consecutive night.
Peralta (6-5) used a 96-98 mph fastball and his nasty slider to hold scuffling David Wright and the punchless Mets to four hits in 6 1-3 innings. The right-hander won his second consecutive start following a four-game losing streak.
It was the second time Peralta has shut down the Mets. He beat them 3-0 with eight innings of two-hit ball at Miller Park on Sept. 16, 2012.
''Wily was really good. Command a lot better. Fastball was down in the zone better. Slider was better,'' Roenicke said. ''I thought he pitched today instead of fighting through things and just trying to throw as hard as he could.''
Will Smith worked a scoreless eighth and ex-Mets closer Francisco Rodriguez got three quick outs for his 20th save in 22 attempts. First baseman Mark Reynolds made a diving catch to end it.
Milwaukee has won nine of 14 overall.
''It was definitely a grind-it win,'' Lucroy said.
In his second game since moving into the leadoff spot, Scooter Gennett gave the Brewers a pair of pesky at-bats that paid off.
He saw a total of 16 pitches during his first two trips to the plate and got a hit both times. After a double to start the third, he scored on a groundout by Lucroy.
With the score tied in the fourth, Mets left fielder Curtis Granderson misplayed Aramis Ramirez's leadoff double. Segura tried to squeeze home a run with one out, but bunted foul. On the next pitch, he lined an RBI single to snap a 2-for-28 skid.
Lucroy's fifth-inning double sent Ryan Braun to third. He scored on Gomez's infield single to make it 3-1.
''Luke's locked in and he has been for quite a while,'' Roenicke said. ''His at-bats are outstanding.''
Taylor Teagarden was called out on a bang-bang play at first to open the bottom half. Collins challenged, and the crowd cheered when replays appeared to show Teagarden was safe by a hair.
But the call stood upon review, bringing a confounded Collins out of the dugout again. He gestured toward the big video board in center field and was given some leeway during the discussion before getting tossed by plate umpire Gary Cederstrom.
It was Collins' first ejection this season. Managers are not allowed to argue replay rulings.
''I knew when I left the dugout what was going to happen,'' Collins said. ''Sometimes you have to have an answer.''
Lucas Duda's sacrifice fly put the Mets ahead in the second.
NOTES: Gomez has reached safely in 26 straight games, the longest active streak in the majors. ... Milwaukee must decide by Friday whether to return LHP Tom Gorzelanny (shoulder surgery) from his rehab assignment or keep him on the disabled list. ... An MRI showed Brewers RHP Tyler Thornburg has irritation in his right elbow, but no ligament damage. ''It's not super serious, but we are going to be cautious,'' Roenicke said. Thornburg went on the 15-day disabled list June 7. ... Brewers RHP Kyle Lohse (7-2, 3.27 ERA) faces LHP Jonathon Niese (3-3, 2.68) in the series finale.