The Mets climbed back into the game with a four-run seventh that was extended when the Padres were unable to convert consecutive double-play opportunities.
Manuel Margot came within a triple of the cycle, and fellow rookie Dusty Coleman hit his first major league home run.
Brad Hand worked the ninth, earning his fourth save and pushing his scoreless string to 17 1/3 innings.
Mets outfielder Yoenis Cespedes kneels down after taking a strike during the seventh inning against the Padres on July 27, 2017 in San Diego.
Margot homered and doubled while maintaining a hot streak that has come since his wife gave birth to their son, Diamond, last week.
"When you become a dad, you get more power, you get more pop", the center fielder said jokingly.
Until Monday, the 30-year-old infielder had only five major league at-bats to show for nine seasons in professional ball.
Back in the lineup Thursday, he stretched the lead to 7-1 in the fifth with a three-run blow.
"That was awesome", Coleman said of his blast that carried 417-feet to right center.
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"You love seeing guys grinding so hard their entire life to have moments like that". Right-handed starter Luis Perdomo allowed one run through the first six innings before faltering.
Jay Bruce went 1-for-4 with a two-run home run and three total RBI in Thursday's loss to the Padres.
Flexen's debut didn't improve in the second.
"I told myself at that moment, 'Hey, welcome to the big leagues", Flexen said of Margot's homer.
The righty hit Coleman in the back with an 0-2 pitch in the second and walked No. 8 hitter Torrens to load the bases.
With one out, Margot belted a chest-high fastball off the center-field wall for a double that brought in three runs, the final one unearned. He reached the double-digit victory mark for the first time since 2013 by allowing two runs and four hits.
"It was a tough one to swallow there, a tough outing", Flexen said, "but still living the dream here". Asuaje tried to score and was initially ruled safe by plate umpire Vic Carapazza.
Myers then tried to score from third on a fake double steal, only to be thrown out at the plate by second baseman Wilmer Flores. However, Mets manager Terry Collins challenged the call, and Asuaje was ruled out after a 80-second review.
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