Freddie Freeman singled home the go-ahead run in the 10th.
The wild loss extended the Marlins' losing streak to seven games, their longest since April 2009. Six of the defeats have been by a single run.
After the game Florida announced the firing of batting coach John Mallee. He will be replaced by Eduardo Perez, son of Hall of Famer Tony Perez.
"I don't want to put it all on John, and I don't want to put it all on Eduardo," president for baseball operations Larry Beinfest said. "We just need to find a way to score some runs."
They couldn't against the 37-year-old Lowe, who gave up two hits in 6 innings. He had his sinker working, with 13 of his 20 outs coming on grounders.
"The wind was blowing in my face and making the ball sink," he said with a smile. "It seems like in about the third inning we were able to get in a good rhythm. It's pretty fun when you can throw the ball where you want. It doesn't happen very often."
The Marlins went 1-for-8 with runners in scoring position and are 8-for-54 (.148) in those situations during the first six games of their dismal homestand.
"Every game we've been one hit away from winning," manager Edwin Rodriguez said.
In other games:
* At Milwaukee, Nyjer Morgan drove in the winning run with two outs in the ninth, Prince Fielder hit two homers and the Brewers earned a 7-6 come-from-behind win over the New York Mets.
* At Pittsburgh, Andrew McCutchen led off the 12th with a home run and the Pirates reached .500 with a 3-2 win over the Arizona Diamondbacks.
* At San Francisco, Matt Cain (5-4) overpowered Washington with 11 strikeouts in his first complete game of the season and also hit an RBI double that helped the Giants beat the Nationals, 3-1, for their sixth win in eight games.
* At Cincinnati, Carlos Pena and Aramis Ramirez hit homers on consecutive pitches in the fourth inning to back strong pitching by Ryan Dempster (5-5) and the Cubs snapped an eight-game losing streak with a 4-1 win over the Reds.
* At San Diego, Troy Tulowitzki hit a two-run double off closer Heath Bell with one out in the ninth inning and the Colorado Rockies beat the Padres, 5-3.
In Padres news, prized prospect Anthony Rizzo, 21, will be called up today in a move to boost the offensively challenged club. The slugging first baseman spent just 2 months at Triple A Tucson.
* At Houston, Bud Norris took a no-hitter into the seventh inning and teamed with Mark Melancon to hold the St. Louis Cardinals to two hits in the Astros' 4-1 win. Norris (4-4) pitched eight scoreless innings, allowing only Lance Berkman's solo homer.
* Jose Pagan, who drove in the eventual winning run for Pittsburgh in Game 7 of the 1971 World Series, has died. He was 76. Pagan also played for the Phillies during 15 seasons in the majors.