Clement's solo shot in the top of the ninth provided a key insurance run for the Pirates, who raised their season's record against the Cubs to 5-0 with the win and took their second straight at Wrigley Field.
Maholm (3-3) allowed only two runs on eight hits over six innings, issuing no walks and fanning four en route to the victory.
Octavio Dotel registered his seventh save of the year despite allowing a run in the ninth. He fanned Ryan Theriot and Marlon Byrd in succession to end the game with the tying run on third.
Ryan Church drove in a pair of runs and Andrew McCutchen got the Pirates' other RBI.
The struggling Cubs lost for the ninth time in 11 games. Chicago starter Ryan Dempster (2-4) yielded three runs on four hits over seven innings in the defeat.