The new fan favorite at Citi Field, Flores hit a leadoff homer in the 12th inning to lift the New York Mets over the Nationals 2-1 Friday in the opener of a pivotal series between the top teams in the NL East.
Harvey took a shutout into the eighth, and the Mets pulled within two games of first-place Washington.
"The problem is we extended guys in the bullpen. See if we can make an adjustment on that tomorrow," Nationals manager Matt Williams said.
Harper was ejected in the 11th inning after taking a called third strike and screaming right in the face of Meals.
"Just sticking up for my team, and myself, at the same time. He was bad all night," the slugger said.
Harper, now 0 for 17 against Harvey, had reached base safely in a career-best 26 consecutive games before going hitless in five at-bats. The fourth-year outfielder has been tossed six times in his career, three this season.
"He needs to stay in the baseball game," Williams said. "We talked about it. We'll talk about it again."
Yunel Escobar tied it in the eighth with a two-out RBI single on Harvey's final pitch. Ex-Nationals reliever Tyler Clippard then needed 13 pitches to strike out Jayson Werth looking on a fastball at the knees.
Carlos Torres (4-4) struck out the side in the 12th. Nationals batters whiffed 16 times and went 1 for 8 with runners in scoring position.
Two nights after endearing himself to Mets rooters when they saw him wiping away tears at shortstop after he thought he'd been traded, Flores received four standing ovations on an invigorating day for the Mets.
A few minutes before the 4 p.m. trade deadline, the Mets gave their meager offense a major boost by obtaining slugger Yoenis Cespedes from Detroit for two minor league pitchers.
Hours later, Flores drove in both Mets runs and made a spectacular play at second base.
Flores sent a 1-1 fastball from Felipe Rivero (1-1) to left-center for his 11th home run and first in 147 at-bats since June 12 against Atlanta. Frenzied fans in the crowd of 36,164 jumped out of their seats and roared as Flores pumped his arm and circled the bases. Some chanted "Wil-mer Flores! Wil-mer Flores!" as they filed out of the ballpark.
"It was just a tough situation to run out our bullpen like that," said Gonzalez, who walked four in 4 2-3 innings. "This is on me. I should have gone deeper into the game and gave us a chance."
Harvey retired his first 16 batters before Jose Lobaton singled in the sixth, prompting a collective groan and then a warm hand. The right-hander retired 30 straight Nationals hitters dating to his July 20 start in Washington, a 7-2 loss to Gonzalez.
Harvey owns a 0.99 ERA in eight career outings against the Nationals, the lowest mark for any pitcher with at least five starts vs. the Expos/Nationals franchise. This time, he was backed by a string of exceptional defensive plays.
Flores stretched out for a diving stop in the first, earning his initial standing ovation. Third baseman Juan Uribe made a leaping grab in the third, and right fielder Curtis Granderson a sliding catch in the fourth. Gold Glove center fielder Juan Lagares ran down Desmond's two-out drive at the 380-foot sign with a runner on second in the seventh.
A DIFFERENT VIEW
Dan Uggla entered at first base in the 11th. During 10 years in the majors, he had never played anywhere but second.
Nationals: RHP Stephen Strasburg (left oblique strain) is slated to throw 80-85 pitches Monday in his second rehab outing for Triple-A Syracuse.
Mets: C Travis d'Arnaud went 0 for 4 with a walk in his return from the disabled list. ... LF Michael Cuddyer (left knee inflammation) is expected to begin playing rehab games in the next few days.
Nationals rookie Joe Ross (2-3, 3.03 ERA) starts the middle game of the series against All-Star Jacob deGrom (10-6, 2.05). The last time they matched up on July 21 in Washington, deGrom and the Mets won 7-2. Over his past 12 starts, deGrom has a 1.37 ERA.