Fukudome's hit scored Starlin Castro to produce a 2-2 tie and one batter later Colvin chased Fukudome home with the go-ahead score.
Fukudome finished 3-for-3 with two runs scored while Castro and Darwin Barney each contributed a pair of hits for the victors.
Cubs starter Tom Gorzelanny was struck in the pitching hand with a line drive in the third inning and exited the game after 2 2/3 scoreless innings. Tom Diamond (1-3) collected the win despite yielding a pair of runs over 1 2/3 innings in an emergency appearance.
Four subsequent Cubs hurlers held the Pirates to one unearned run over 4 2/3 frames, with Carlos Marmol picking up his 25th save.
Neil Walker homered and went 3-for-5 for the Pirates. Pittsburgh starter James McDonald (2-5) surrendered three runs on eight hits in five innings.