Flores smacked a two-run homer over the left-field wall off the Cubs' Zac Rosscup with one out in the eighth at Cashman Field. The Mets tacked on one more run in the inning and two in the ninth.
Mets starter Bartolo Colon, who signed a $20 million-two year deal in the offseason, started strong then struggled. He gave up seven hits, four runs (all earned), had one walk and no strikeouts in four-plus innings.
Anthony Rizzo hit two solo homers off Colon.
Mets: Colon, 40, is in his first year with the Mets after a stellar 18-win season with the Oakland A's last year. Earlier this spring, the hard-throwing right-hander was sidelined by a minor calf injury.
"Colon still has solid stuff," manager Terry Collins said. "He is exactly as advertised. He's a throwing machine and will make a big difference for us this year."
Cubs: Wada, a rookie left-hander, was rocked in the first inning. He gave up five hits, four runs (all earned) and had two walks in three innings. Right-hander Carlos Pimentel took over in the fourth and helped the Cubs get back into the game.
Saturday was a special day for Kris Bryant, the Cubs No. 1 pick (second overall) in last year's major league draft. Bryant was a slugging phenom at local Bonanza High and later went to star at the University of San Diego. Bryant, who was sent down to minor league camp Wednesday, didn't play Saturday but may play Sunday.
In an unusual bit of scheduling, the Cubs have begun a three-day stretch of six split-squad games, with the Mets the only common opponent. Of those games, only two are in Mesa, Ariz. The Cubs have already had two split-squad dates (March 1 and 7) and will have one more after Monday (March 25). On the other hand, this is the Mets first split-squad engagement of the year. They only have one more remaining in the season (March 23).