The Mets broke a 4-all tie in the seventh. Luis Avilan (1-1) gave up a leadoff single to Daniel Murphy, who scored on a two-out single by Juan Lagares off Gus Schlosser. Murphy drove in three runs with three hits.
Led by Young, the Mets stole five bases. Young also used his speed to lead off a two-run third inning with a bunt single.
Upton drove in three runs with three hits. Older brother B.J. Upton hit a triple after receiving pregame batting tips from former Braves star Chipper Jones.
Jones, in his second year of retirement, talked with B.J. Upton about eliminating an extra ''hinge'' in his swing.
Manager Fredi Gonzalez said he ''threw a little chum in the water'' when he invited Jones. Gonzalez said Jones ''has got a little itch'' to spend more time with the team.
B.J. Upton, who took a .138 batting average into the game, had help on his triple when right fielder Curtis Granderson appeared to lose the ball in the lights as the ball went over his head. It was his only hit.
Justin Upton's second homer, a two-run shot deep into the left-field seats in the third inning, gave the Braves a 4-3 lead.
Mets starter Jenrry Mejia, obviously frustrated, slapped his mitt and then threw the glove to the grass. Upton's first homer, to lead off the second, landed in the first row beyond the right-field wall.
Mejia gave up four runs in five innings on six hits and four walks. Atlanta's David Hale also had control problems as he gave up four runs, three earned, in 4 1-3 innings on five hits and five walks.
The Mets tied the game in the fifth on a leadoff triple by Young and Murphy's single. The Mets loaded the bases on two walks by Hale, but reliever Anthony Varvaro struck out Lagares and ended the inning on Travis d'Arnaud's groundout.
''We made a decision, and you don't have much credibility if you keep changing your mind every other day because someone goes 2 for 4,'' Collins said before the game.
Braves shortstop Andrelton Simmons was held out with a jammed right wrist. Simmons was listed in the original lineup and was removed following batting practice. The Braves said he was hurt in Wednesday night's game and is day to day.
Ramiro Pena, making his first start of the season, replaced Simmons and had one hit.
NOTES: Former President Jimmy Carter and his wife, Rosalynn, sat near the Braves' dugout. ... Hale is Atlanta's first starting pitcher to give up more than two runs this season. ... Mets OF Chris Young (tight right quad) was 2 for 2 with two singles while playing five in an extended spring game in Port St. Lucie. He also had two walks and a sacrifice fly. ... RHP Dillon Gee will be on the mound when the Mets open a weekend series at the Angels, who will start LHP Tyler Skaggs, on Friday night. ... Atlanta RHP Julio Teheran will face Washington RHP Tanner Roark as the Braves' homestand continues.