Donovan Solano's pinch-hit single off Kimbrel drove in the go-ahead run in the ninth, and Miami beat Atlanta 4-3 on Thursday night.
It was the Braves' first loss of a three-game series at Turner Field this season and their first loss of a home series to the Marlins since April 12-14, 2011.
Kimbrel (2-2) alternated walks and strikeouts for the first four batters. He walked Ed Lucas and Logan Morrison, and struck out Giancarlo Stanton and Marcell Ozuna.
Solano, hitting for Derek Dietrich, singled to right field. Lucas scored from second, beating Jason Heyward's throw to the plate.
"Any time you start an inning off with a leadoff walk and then you put another one behind it, that makes it difficult," Kimbrel said.
Solano hit a 0-2 pitch from Kimbrel.
"It wasn't down as much as I would have liked," Kimbrel said. "It's one of those pitches that when you throw it, you kind of want to throw it in the dirt. You don't want to throw it where he can put the bat on the ball. And he was able to do it."
The Marlins, who snapped a streak of eight straight losses to the Braves with Wednesday night's 6-3 victory, won two of three in the series.
"It sure feels good, and I know the guys are fired up," said Marlins manager Mike Redmond.
"You've got to earn wins in this place against this team, and we earned it."
Ozuna had three hits, including a homer, and drove in two runs for Miami.
A.J. Ramos (3-2) allowed one hit with four strikeouts in two scoreless innings. Steve Cishek pitched the ninth for his 17th save.
Cishek walked Freddie Freeman to open the ninth. With one out, Stanton made a lunging catch of Dan Uggla's drive to the right-center gap to preserve the lead.
"Stanton made a hell of a play there," said Braves manager Fredi Gonzalez. "I don't know how the ball stayed up in the air that long."
Redmond called Stanton's play "one of the best catches I've ever seen" before adding with a laugh "I knew he had it all the way."
Cishek stood on the mound, watching the line drive head toward the gap, and just hoped for a miracle from Stanton.
"I saw he got a pretty good jump on it," Cishek said. "It was like slow motion, and I was wishful thinking 'Reach for that thing, big fella.' I got fired up."
Cishek struck out B.J. Upton to end the game.
Miami has won eight of its last 10 overall for four straight series wins.
Henderson Alvarez came off the 60-day disabled list for his Marlins debut and gave up hits to four of the first five batters to open the game. Freeman's single drove in Andrelton Simmons and Heyward. Freeman scored on Brian McCann's double for a 3-0 lead.
Alvarez made a quick recovery to retire the next 11 batters, providing his teammates an opportunity to rally against Julio Teheran.
Ozuna hit his fifth homer in the second inning. Jeff Mathis singled to lead off the second and scored on a groundout by Lucas. Ozuna added a fourth-inning single to drive in Morrison, who doubled, for a 3-all tie.
In his shortest outing since lasting five innings on April 18 at Pittsburgh, Teheran gave up six hits and three runs in five innings. He struck out seven.
"The whole game I was battling out there," Teheran said, adding a high pitch count led to his early exit.
"I think I had almost every batter 3-2," he said. "They were swinging and there were a lot of foul balls. I think that's why I had a lot of pitches.
"I wasn't commanding my breaking ball so they were just sitting on my fastball and two-seamer."
Alvarez also allowed three runs in five innings. He gave up five hits with no walks.
Alvarez was lifted for a pinch hitter in the sixth when the Marlins had runners on first and third with one out. Greg Dobbs popped out and David Carpenter ended the inning on Justin Ruggiano's groundout.
NOTES: The Braves optioned RHP Cory Gearrin to Triple-A Gwinnett after the game and will make a corresponding move on Friday. ... The Marlins optioned RHP Tom Koehler to Triple-A New Orleans to clear a roster spot for Alvarez. Koehler was 1-5 with a 4.70 ERA in 16 games, including 10 starts. ... Braves C-OF Evan Gattis, recovering from a right oblique injury, took swings off a tee. Gattis has been on the 15-day DL since June 18. ... The Braves placed OF Jordan Schafer on the 15-day DL with a right ankle contusion. He has been limited since fouling a ball off his ankle on June 26. OF Joey Terdoslavich was called up from Triple-A Gwinnett and struck out as a pinch hitter in the eighth. ... RHP Tim Hudson will face LHP Cliff Lee when the Braves open a series at Philadelphia on Friday night. ... Miami's road trip shifts to St. Louis, where RHP Jacob Turner will face Cardinals RHP Jake Westbrook on Friday night.