Nova (9-6) held the Cubs to two runs in 6 2/3 innings. He struck out six and walked one.
Josh Bell went 3-for-4 with two doubles on the one-year anniversary of his major-league debut. Felipe Rivero earned his sixth save.
Kyle Schwarber and Ian Happ homered for Chicago. Schwarber hit his first home run since he returned to the Cubs following a demotion to Triple-A Iowa, as Chicago tried to win consecutive games for the first time since June 18-20.
The Pirates claimed a 3-2 lead on Polanco's eighth home run, a two-run shot, in the sixth inning. Bell scored after leading off with his second double. Francisco Cervelli scored from first on Jordy Mercer's double later in the inning.
Cubs starter Jake Arrieta (8-7) allowed four runs (three earned) and six hits in 5 2/3 innings. He was coming off his best start of the season, limiting the Cincinnati Reds to one hit in seven shutout innings.
Arrieta was 0-3 with a 7.81 ERA in his previous five starts against Pittsburgh after he went 9-1 with a 1.46 ERA in his first 12 starts versus the club.
The Cubs left runners at the corners in the eighth after pinch hitter Tommy La Stella doubled and advanced on a groundout before Kris Bryant drew a walk.
Happ and Schwarber hit back-to-back home runs to give the Cubs a 2-1 lead in the fourth. Schwarber hit his 13th home run of the season two pitches after Happ connected.
The Cubs have hit consecutive home runs three times this season. Happ has at least one hit in 16 of his last 18 games.
The Pirates held a 1-0 lead in the top of the fourth on a Cervelli groundout with runners at second and third. Bell led off with a double and David Freese was hit by a pitch before they advanced on a passed ball. Bell scored an unearned run on Cervelli's grounder to third base.
NOTES: Pirates LHP Antonio Bastardo (0-1, 15.00 ERA) was designated for assignment Saturday. He allowed two runs in an inning Friday against the Cubs. Opponents scored off Bastardo in eight of his nine appearances. ... The Pirates recalled INF Phil Gosselin from Triple-A Indianapolis to take Bastardo's place on the roster. Gosselin was batting .287 at Triple-A, and playing shortstop benefitted him, manager Clint Hurdle said. Gosselin hit .135 in 24 previous games with the Pirates this season. ... Cubs RHP Kyle Hendricks (hand tendinitis) will pitch on a rehab assignment Monday with Double-A Tennessee, manager Joe Maddon said. Hendricks has been on the disabled list since June 5. ... Cubs LHP Mike Montgomery, who has been a starter, will be available out of the bullpen Sunday, Maddon said. ... The order of the Pirates starting rotation after the All-Star break will be RHPs Gerrit Cole, Chad Kuhl, Trevor Williams, Jameson Taillon and Ivan Nova.