NEW YORK -- Craig Kimbrel hardly ever needs help with the ninth inning. He got some Saturday night.

Jordan Walden nailed down the final out with the bases loaded after Atlanta Braves manager Fredi Gonzalez pulled his star closer following a shaky performance in a 7-5 win over the New York Mets.

Sidelined recently by shoulder discomfort, Kimbrel threw 24 pitches during his first outing in a week. The Braves didn't want him to go any longer, and Gonzalez thought the reliever was rusty.

"The good thing is that we got him on the mound and got him pitching and we'll go from there," Gonzalez said, adding that Kimbrel was pain-free. "He was fine. He was good. That's a good, positive sign."

Freddie Freeman had three hits and hustled his way through a weird play that brought the Braves two runs when the Mets were unable to challenge a costly incorrect call.

Ervin Santana pitched seven crisp innings for his second win over New York in three starts with Atlanta.

Justin Upton hit a three-run homer in the ninth to make it 7-3, and that became crucial when the Mets rallied against Kimbrel.

They scored twice off the hard-throwing right-hander, who loaded the bases with a two-out walk to Lucas Duda. That's when Gonzalez went to the mound and lifted Kimbrel, who wasn't happy about it.

"That's what makes him good," Gonzalez said. "At that point of the game he don't care about his arm, he don't care about anything, but he wants to finish that inning."

Kimbrel waited an extra moment or two before reluctantly handing over the ball.

"I'm a competitor and anytime you get taken out, obviously you get upset about it and I did," said Kimbrel, who apologized to Gonzalez after the game. "That's disrespectful to him, to the team and it's just not the type of person I am and I felt awful about it."

Walden retired Travis d'Arnaud on a grounder to secure his first save of the season and Atlanta's seventh victory in eight games. Gold Glove shortstop Andrelton Simmons was shaded toward the hole and made a strong throw to get d'Arnaud.

"I was ready. I'm always ready," Walden said.

Santana (2-0) allowed one run and struck out seven, giving the Braves their latest outstanding start. Despite several significant injuries in spring training, Atlanta's rotation entered with a 1.47 ERA -- best in the majors by nearly a full run.

David Wright, Daniel Murphy and Chris Young all had three hits for the Mets, held to one by Aaron Harang and two relievers in the series opener Friday night.

Bartolo Colon (1-3) gave up three runs in seven innings for New York.

Young cut it to 4-2 with an RBI single in the eighth off David Carpenter. Duda made a bid for a three-run homer with a long drive that was caught on the warning track in right field.

"I thought it was a home run," Mets manager Terry Collins said. "I thought he hit that ball good."

A single by d'Arnaud brought the Mets within one, but Carpenter ended the inning by retiring Ruben Tejada on an easy grounder with runners at the corners.

Upton's fifth homer came off Jose Valverde and followed an intentional walk to Freeman.

Atlanta was trailing 1-0 with two outs in the third when Freeman fisted a soft bouncer between the mound and home plate. Colon appeared to be in no particular rush to pick it up -- and then he threw wildly past first base as Freeman hustled down the line.

Two runners scored on Colon's error, and Freeman was credited with an infield single. But replays showed the ball hit Freeman's front foot before bounding onto the grass, so it should have been ruled foul.

Collins could not challenge the call because only batted balls that "first land at or beyond the set positions of the first or third base umpire" are subject to video review for fair or foul, according to baseball's replay rules. Since the ball rolled right in front of the plate, the Mets had no recourse.

"Nobody saw it and you can't challenge it," Collins said. "You have to understand that this is a whole work in progress."

Freeman doubled home a run in the fifth, and Upton scored on Daisuke Matsuzaka's wild pitch in the eighth to make it 4-1.

Game notes
Braves LHP Mike Minor (left shoulder tendinitis) gave up two earned runs in six innings during a rehab start for Triple-A Gwinnett. He could come off the disabled list next week. ... Backup outfielder Jordan Schafer injured the middle finger on his right hand but said he got X-rays and everything is fine. ... Young doubled in the fourth for his first hit with the Mets.