Maholm (2-7) earned his first win since April 25, walking none and striking out four in his third career shutout. The left-hander retired the first 13 Cubs batters and allowed only one runner to reach second base in his 91-pitch gem.
Ronny Cedeno hit a three-run shot in the fourth inning -- the first of four long balls struck by the Pirates, who clinched their three-game series at Wrigley Field with the win.
Lyle Overbay and Chris Snyder hit bases-empty homers and Andrew McCutchen added a two-run bomb in the seventh for Pittsburgh.
Randy Wells (1-1), making his first start in nearly two months after coming off the disabled list, was roughed up for five runs on five hits over four innings for the Cubs.