Milwaukee produced four home runs, with Maldonado's blast in the fourth putting the Brewers ahead for good at 4-2. Corey Hart hit solo shots in both the first and fifth innings and Taylor Green added a two-run homer in the seventh.
Milwaukee took a 9-3 lead into the ninth before San Diego came up with two runs on a triple by Logan Forsythe. Two of the other three San Diego runs were driven in by Everth Cabrera with the unique combination of an inside-the-park homer in the third and a bases-loaded walk in the fourth.
The Brewers won their third straight and handed the Padres their third loss in a row.
Milwaukee starter Shaun Marcum (5-3) survived 5 2/3 innings to get the win while giving up three runs on six hits. The Brewers got to Edinson Volquez (2-6) for six runs on six hits in five innings.
The Brewers and Padres played the only National League game Friday at the start of another round of interleague play.