Bourn was a home run shy of the cycle, going 3-for-4 with three RBIs, in the Astros' 7-3 victory over Silva and the Cubs.
Chicago lost for the second time in six games this month and dropped to 9-5 under Mike Quade, who took over on Aug. 23 for Lou Piniella. The Cubs were minus both rookie Starlin Castro, third in the National League with a .317 average, and third baseman Aramis Ramirez. Castro was sitting for the second straight day after a baserunning mistake, while Ramirez was nursing a sore right quad.
Castro may return on Wednesday for the series finale.
"I will sleep on that tonight and contemplate," Quade said. "He's had a couple good days and done extra work and has had some time. There's a fine line between observing for too long and getting better, so we'll see."
Silva (10-6) did feel better despite serving up six runs, which matched his season high. He gave up nine hits over five innings and threw 87 pitches.
"First time out, stuff-wise, he did OK," Cubs catcher Koyie Hill said. "His changeup was good. He had confidence in his pitches. It's a good first step back toward getting back to where he normally is."
Silva wasn't satisfied.
"I felt very good," Silva said. "I didn't enjoy the result."
Bourn tripled to lead off the game and scored on Jeff Keppinger's single, but the Cubs answered in their half to go ahead, 2-1, on Marlon Byrd's RBI single and a run-scoring fielder's choice by Tyler Colvin against Nelson Figueroa (5-2).
Brett Wallace hit his first Major League home run with one out in the Houston second. Tommy Manzella and Jason Castro followed with singles, and both scored one out later on Bourn's double to go ahead, 4-2.
Colvin's RBI triple with one out in the third closed the gap to 4-3, but the Astros rattled off three straight hits in the fifth, including an RBI single by Keppinger and an RBI double by Hunter Pence, to go ahead, 6-3.
"We got started quick on [Silva] and were able to keep them down," Bourn said. "They came back and they fight over there, even without having [Derrek Lee] in there and Ramirez. ... We were able to hold them off and poured it on even after we had four and were able to get to seven, and that was enough for our pitching staff to hold us down."
Quade said he hoped Silva had time to build up arm strength in the final four weeks of the season. The Cubs are still unsure as to when left-hander Tom Gorzelanny will return after getting hit on the left little finger by a line drive.
"It's late [in the season], but you hope that through more activity his arm strength will be better and his stuff will be better as well," Quade said.
Silva has had a roller-coaster season, beginning with an 8-0 start, then hitting a rough stretch and suddenly finding himself in a Denver hospital because of his heart. Now, the goal is to finish strong for 2011.
"That's what I'm looking for is to try to finish very strong and next year, be ready to go," Silva said. "That means a lot for any player, the way you finish."