Travis Shaw opened the Brewers' ninth with a double flared down the left field line with the Padres shifted to the right side. Shaw moved to third when Domingo Santana lined a single off the glove of shortstop Erick Aybar.
Bandy then bounced a single through the left side, scoring Shaw. After a fourth straight single by Keon Broxton loaded the bases, Santana scored the inning's second run when Orlando Arcia grounded out to third.
Jacob Barnes (1-0) threw one scoreless inning for the win, and Corey Knebel pitched the ninth for his second save.
Maurer (0-3) has given up nine runs on 11 hits in 2 2/3 innings over his past four appearances.
Earlier, the game was a pitching duel between right-handed starters, Milwaukee's Matt Garza and San Diego's Jhoulys Chacin.
Each allowed one run. Garza worked six innings and gave up four hits and a walk while striking out three. Chacin gave up two hits and two walks with a season-high eight strikeouts in seven innings.
Shaw, who missed the first two games of the series with a sprained index finger on his right hand, returned to the Brewers' lineup and drove in the game's first run.
Eric Sogard drew a walk to open the game and moved to second on a ground single up the middle by Hernan Perez. After Jesus Aguilar struck out, Shaw singled to center off Chacin.
Only two of the first 16 hitters Garza faced reached base. Manuel Margot opened the Padres' first with a single, and Hunter Renfroe walked in the second. Garza retired nine consecutive hitters before rookie Allen Cordoba tripled with two out in the fifth.
The Brewers were still clinging to their 1-0 lead with two out in the sixth when Wil Myers beat out an infield single to short. Yangervis Solarte followed with a short fly to center that landed just in front of the glove of the sliding Broxton then bounced behind the center fielder, allowing Myers to score from first on a double.
Meanwhile, Chacin retired 19 straight Brewers between Shaw's run-scoring single in the first and a two-out walk to Bandy in the seventh.
NOTES: The Padres placed RHP Trevor Cahill on the 10-day disabled list due to inflammation in the posterior side of his right shoulder. To replace Cahill on the 25-man roster, San Diego recalled RHP Kevin Quackenbush from Triple-A El Paso for the fourth time since April 14. ... RHP Jarred Cosart will make Cahill's scheduled start Thursday afternoon in the series finale against the Brewers and RHP Zach Davies. ... Milwaukee manager Craig Counsell said RHP Wily Peralta, who has a 6.08 ERA in eight starts, is moving to the bullpen. Peralta was scheduled to start Friday, but that opportunity will likely go to RHP Paulo Espino, who is with Triple-A Colorado Springs. ... OF/1B Eric Thames (strep throat) was feeling better Wednesday, but he likely won't return to the Brewers' lineup until Friday against the Cubs in Chicago.