George Kottaras led a balanced attack with 5, to sweep the season series.
Ryan Braun hit a solo homer for the Brewers, who set a franchise record for most home victories in a season with 55. The 1978 team held the previous mark at 54-27.
The Brewers hold a one-game lead on Arizona in the race for the second-best record in the National League and home field advantage in the first round of the postseason. Milwaukee host the Pirates, while the NL West-champion Diamondbacks are at home against the Dodgers for a three-game set to conclude the season.
Chris Narveson (11-8) allowed four runs on five hits over 6 1/3 innings to pick up the win for Milwaukee, which took all seven games from the Marlins this year to sweep the season series for the first time since their first meeting in 1998.
Ricky Nolasco (10-12) got blasted to the tune of seven runs -- six earned -- on nine hits over two-plus innings.
"I just need to focus on getting better for next year," Nolasco said.
Bonifacio's blast to left-center field in the first inning gave the Marlins an early lead.
But the Brewers took the lead for good with a three-run second. Rickie Weeks singled and Jerry Hairston Jr. reached first on Matt Dominguez's fielding error to begin the frame. With one out, Kottaras, Narveson and Corey Hart hit three straight RBI singles for a 3-1 edge.
Milwaukee added four runs in the third to create some distance. Braun, Prince Fielder and Weeks started the frame with three consecutive singles to plate a run. Hairston's double plated another run. Sandy Rosario came in from the bullpen and gave up an RBI single to Yuniesky Betancourt. Kottaras' RBI fielder's choice made it 7-1.
Braun made it a seven-run game with a homer to right in the fourth. Murphy got the run back with a blast to right-center in the fifth.
"It's tough to pitch with that kind of lead," Narveson said. "You have to really focus. Sometimes games just get away from you in that type of situation."
Omar Infante's two-run double in the seventh cut the gap to 8-4. But Craig Counsell's RBI fielder's choice in the home half made it a five-run contest.
Dominguez's RBI double in the eighth accounted for the final margin.
Nolasco fell to 1-2 in six career starts against the Brewers...Narveson improved to 1-2 in four career starts against the Marlins...Florida has not been swept in a season-series by a National League team since that '98 season, when they went 0-9 against Cincinnati, the Brewers and San Francisco.