Rene Rivera and Michael Conforto each hit an RBI double during a three-run fifth against starter Matt Garza (2-2). Sandwiched in between, Gsellman drove in the go-ahead run with a sacrifice fly.
He also drew a bases-loaded walk from reliever Rob Scahill in the sixth, the eighth for New York this season after totaling three last year.
Wilmer Flores added three hits for the Mets, who had a quick turnaround after landing in New York at 2 a.m. following Sunday night's victory at Pittsburgh. Still, they handed the surprising NL Central leaders their sixth loss in eight games as the teams opened a four-game series.
Before the game, general manager Sandy Alderson said Gsellman (3-3) probably is headed back into a struggling bullpen when injured starters Steven Matz and Seth Lugo come off the disabled list, likely after one more minor league rehab outing apiece.
"We do think he can help us there," Alderson said about Gsellman. "With a 5.00 ERA in the bullpen, a lot of people can help us."
The relief corps came through this time, though.
Rookie righthander Paul Sewald fanned two in a perfect eighth, and Addison Reed got three outs for his seventh save in nine chances. Reed, who blew a save opportunity in his previous outing Saturday at Pittsburgh, gave up consecutive singles to start the ninth before retiring the next two batters — including two strikeouts.
Domingo Santana homered on an 0-and-2 pitch from Gsellman, one day after hitting Milwaukee's first grand slam of the season in Sunday's victory over Arizona.
That was the only earned run Gsellman permitted. He struck out five and walked two.
Mets shortstop Asdrubal Cabrera committed a throwing error that led to the Brewers' first run on a groundout by Keon Broxton. Cabrera, however, made amends with a single to start New York's three-run fifth.
Garza gave up four runs and seven hits in 52/3 innings.
Milwaukee swept three games from the Mets at home May 12-14.
Slumping Brewers first baseman/outfielder Eric Thames made his fourth start of the year in left field after getting a day off Sunday. He went 0-for-3 with a walk and is hitless in his last 19 at-bats.
Mets second baseman Neil Walker was rested in favor of Flores.
Mets: Rivera crouched in pain after getting hit on the right wrist but remained in the game. ... Matz and Lugo have both been out all season with elbow trouble. ... Alderson said the team hopes slugger Yoenis Cespedes (strained left hamstring) will be ready to come off the disabled list in a week to 10 days — perhaps in time to be the DH during a two-game series at Texas that begins June 6.