Gonzalez rested Simmons, third baseman Chris Johnson and catcher Brian McCann.
The Braves had only one hit, a single by Paul Janish in the second, before scoring once in the fifth, on Upton's sacrifice fly.
NOTES: LF Eric Young Jr., who was 0 for 5, was the only Mets starter without a hit. ... Braves CF Jordan Schafer, who has a bruised left quadriceps, was removed from the original lineup. ... The Braves completed a 7-2 homestand. ... Mets manager Terry Collins said he doesn't expect 1B Ike Davis to return this season from his strained right oblique. Davis had an anti-inflammatory injection on Tuesday in New York. ... Collins said 3B David Wright has made progress but has no projected date for his return from a strained right hamstring. ... Both teams are off on Thursday. The Mets open a series in Cleveland on Friday night when RHP Zack Wheeler faces LHP Scott Kazmir. The Braves play at Philadelphia Friday night as LHP Mike Minor faces LHP Cliff Lee.