Pence's first career multihomer game featured a three-run shot in the fourth and two-run drive in the sixth. The homers gave the standout rookie 14 for the season, while helping Rodriguez (8-12) win for the first time since July 26.
Cooper replaced the fired Phil Garner on Monday. And with a month left in the season, Houston is 13 games under .500 but only eight games back of the first-place Cubs in what is becoming a tightly bunched NL Central.
Rodriguez, who'd been 0-3 in six previous August starts, allowed four hits and earned a rare road victory. He is 2-9 away from Minute Maid Park and 6-3 at home.
Chicago broke up the shutout bid in the eighth when pinch-hitter Daryle Ward had an RBI single, one of three straight hits in the inning off reliever Dave Borkowski.
Trever Miller got the final out in the eighth and pitched a perfect ninth in a non-save situation.
Pence, who came off the disabled list 10 days ago, hit his second homer of the game in the sixth off Cubs reliever Michael Wuertz.
His two-out, three-run homer off Sean Marshall capped a fourth that started when third baseman Aramis Ramirez fumbled Ty Wigginton's grounder for an error. After Chris Burke singled, Marshall got two outs before Pence hit a long drive to left for a 4-0 Astros lead.