Fielder's fourth home run of the season, a mammoth, 428-foot shot to dead center off Pinto (1-1), broke a 3-3 tie in the bottom of the eighth. Pinto had not allowed a run in his previous 11 appearances.
"He made a mistake to a pretty good hitter and he hit it out of the ballpark," Marlins manager Fredi Gonzalez said. "I'd rather that happened than a guy walk the bases loaded and walk three guys in. He went after him and this time Prince won."
Pinto had been scored on in just one of his previous 12 outings.
It was Fielder's second winning home run in four days. He also homered twice against Philadelphia on Wednesday, with the game-winning blast coming in the eighth inning of a 5-4 victory.
Known more for power after his 50 home runs led the NL last season, Fielder showcased his base running by scoring three times, including an unlikely run on a suicide squeeze in the second.
"That's my first time ever doing that," he said. "I timed it perfectly so they didn't notice it right away. For the first time, it was pretty good."
Villanueva squared away on a low fastball and then ran, more out of survival than anything else.
"I saw Prince coming out of the corner of my eye," he said. "I just bunted the ball and got out of the way. He was probably going to run me and the catcher over."
Fielder was happy that Villanueva got the bunt down.
"I am just happy he knew to bunt," Fielder said. "He was able to help himself right there to get a run."
Fielder's run tied the game and ended a string of 16 consecutive innings without scoring for the Brewers.
Eric Gagne dominated the ninth by striking out the side for his seventh save in 11 chances.
Hanley Ramirez hit a solo shot in the first for his eighth home run, his third leadoff homer this season.
Milwaukee stopped Hendrickson from picking up his fifth win. The 6-foot-9 left-hander had given up only seven total earned runs while winning a career-best four straight starts. He surrendered three runs -- two earned -- in six innings. He struck out three and walked one.
"Too bad we couldn't score any runs for him," Gonzalez said.
Milwaukee's Villanueva went six innings, allowing two runs and six hits with five strikeouts. Lifted for a pinch-hitter, he turned over a 3-2 lead to Torres to start the seventh.
Hendrickson led off the fifth with his first career triple and scored on Uggla's sacrifice fly as the Marlins pulled to 3-2.
Fielder knocked in a run and later scored another as the Brewers went ahead 3-1 in the third.
Marlins first baseman Mike Jacobs fouled off a pitch in the fifth and immediately left the game with a sprained right middle finger. He is day-to-day and will not start against left-hander Manny Parra in the final of the three-game series.
"I iced it a ton and hopefully, it will calm down," Jacobs said.
Milwaukee's last 11 games have been decided by three runs or less. ... Ramirez's homer in the first was the 18th lead-off shot of his career. ... Brewers RHP Ben Sheets threw a bullpen session, the first time he's pitched since leaving a game last week with tightness in his right triceps. He missed his start against Philadelphia on Wednesday because of lingering soreness. If there are no problems, he is scheduled to start against the Chicago Cubs on Tuesday. ... The Brewers drew 44,169 fans for their third sellout of the season.