Tyler Colvin, Micah Hoffpauir, Koyie Hill and Jeff Baker each knocked in a run for the Cubs, who took two of three in the series.
Thomas Diamond (1-3) picked up his first major-league win, despite allowing two hits and two runs in 1 2/3 innings of relief. Starter Tom Gorzelanny exited after 2 2/3 innings when a line drive from Jose Tabata struck his left hand.
Carlos Marmol recorded the final four outs, and fanned three in a scoreless ninth to earn his 25th save.
Neal Walker had three hits including a solo homer while Andrew McCutchen drove in two runs for the Pirates, who have lost five of six.
James McDonald (2-5) took the loss after yielding eight hits and three runs, fanning six and walking two over five full frames.
After Walker’s ninth home run of the season tied the game in the third, the Cubs moved ahead for good in the home half.
Starlin Castro singled with one down and Fukudome followed by doubling him in. Two batters later, a Colvin double plated Fukudome for a 3-1 contest.
McCutchen doubled home McDonald with one out in the fifth to get within a run, but Chicago tallied twice in the seventh on a Hoffpauir RBI single and a base hit from Baker to score Fukudome.
McCutchen’s bases-loaded walk against Marmol in the eighth made it 5-3, but the Cubs closer fanned Tabata to end the frame.
Marmol then struck out the side in the ninth to close out the game.
Hill drove in Darwin Barney, who singled with two out in the second, to get the Cubs on the board.
Tabata’s line-drive with one out in the third deflected off Gorzelanny’s hand before being caught by Chicago second-baseman Blake DeWitt.
Pittsburgh won the season series, 10-5, including five of nine at Wrigley…Mike Quade improved to 6-3 since taking over for Lou Piniella…Prior to the game, the Pirates recalled outfielder John Bowker from Triple-A Indianapolis.