"We have had some trouble scoring runs, so tonight was a breakout to be honest with you, but too far behind to catch up," he said.
Jason Castro homered twice and drove in three runs to lead the Astros to the 8-5 win.
Castro hit a two-run homer in the third inning to push the lead to 5-0, and added a solo shot in the seventh to make it 8-4.
Brandon Barnes gave Houston an early lead with a two-run double in the second inning.
Houston built a 7-0 lead before Toronto got anything going on offence. Kevin Pillar hit his first career homer on a three-run shot in the fifth inning and Edwin Encarnacion had a solo homer in the sixth for the Blue Jays.
Toronto's rally came up short as it tied a season-high with its seventh straight loss.
The Astros jumped on Chien-Ming Wang (1-2) for four hits and five runs in three innings in his first start since July 2 after his contract was selected from Triple-A Buffalo earlier in the day.
"It was a tough go for him," Gibbons said. "He threw some good sinkers, but a lot of them were flat, and that was what they caught up. We fell behind early. It turned out to be too much to overcome."
Brad Peacock (3-4) allowed six hits and four runs in 5 2-3 innings for the win. Chia-Jen Lo pitched a scoreless ninth for his second save.
Castro, who finished with three hits, has 17 homers this season, which ties a team record for home runs by a catcher set by John Bateman in 1966. It was the third multi-home run game of his career and the second this season.
Castro doubled to start Houston's second and advanced to third on a one-out single by Brett Wallace. The Astros took a 2-0 lead on Barnes' two-run double.
A wild pitch by Wang allowed Barnes to advance to third with two outs before he scored when Jonathan Villar reached on an error by Jose Reyes.
L.J. Hoes walked in the third inning before Castro belted his 16th homer to the seats in right field with one out to make it 5-0. Right fielder Rajai Davis climbed up the short wall in vain to chase the ball as it sailed out of his reach and into the stands.
Barnes reached on a second error by Reyes with no outs in the fourth. Robbie Grossman extended his hitting streak to a career-high 11 games with a two-out RBI double before taking third on a passed ball.
Hoes pushed the lead to 7-0 when Grossman scored on his double to the wall in right field.
Peacock allowed a double to Brett Lawrie to start the second inning before retiring the next six batters. Encarnacion walked to start the fourth, but Peacock got out of the inning with a double play.
Peacock allowed consecutive one-out singles to Anthony Gose and Ryan Goins before the homer by Pillar cut the lead to 7-3.
The hit, which bounced off the wall in left-centre field, was originally a double, but it was reviewed and ruled a homer.
Pillar smiled before trotting to home plate where umpire Bill Miller was waiting to hand him the ball.
"The umpire flipping me the ball before I crossed home plate was pretty awesome," Pillar said. "When I got to second base, I thought I hit it pretty good and maybe had a shot of getting over the fence. I tried to play it cool, but eventually, I walked over to the second baseman and shortstop to see if they thought it went over the fence. They just said: 'Oh I don't know'. I just had to wait."
Encarnacion got the Blue Jays within 7-4 when he homered for the second straight game to start the sixth inning.
J. P. Arencibia's RBI double made it 8-5 in the eighth inning.
Wang was making his second career start against Houston and the first since tearing ligaments in his right foot running the bases when he pitched as the ace of the Yankees' staff and faced the Astros on June 15, 2008.
NOTES: The Blue Jays recalled RHP Chad Jenkins from Double-A New Hampshire and transferred infielder Maicer Izturis, out with a sprained left ankle, to the 60-day DL. Jenkins allowed three hits and three runs in four innings. ... The Astros announced LHP Erik Bedard will be moved out of the rotation and into the bullpen. Houston manager Bo Porter said they'll announce his replacement in the rotation early next week. The 34-year-old Bedard, who had never pitched in relief in his career until a stint earlier this season, wasn't too happy about the move. "I was very surprised," he said. "I don't really know what to say."