Tulowitzki went 0 for 4 in his first game at Coors Field since Toronto acquired him from the Rockies last July 27. He received a standing ovation when he batted in the second inning. He stepped out of the batter's box and doffed his helmet to the 36,491 fans.
Gray retired 12 straight and 16 of 17 batters after Travis' homer in the first inning made it 1-0. The Blue Jays made it 4-0 in the third on Josh Donaldson's RBI single and Encarnacion's first homer.
Gray (5-3) settled down to pitch the seventh. He allowed four runs and five hits and struck out eight.
Toronto starter Marco Estrada had allowed three hits before Gonzalez's three-run homer in the sixth -- his 17th -- made it a one-run game. It was his 189th home run with Colorado, moving him past Tulowitzki for fifth on the franchise list.
The Rockies scored six runs in the seventh off three relievers. Drew Storen (1-3) hit two straight batters ahead of Nolan Arenado's two-run single, Jesse Chavez walked Mark Reynolds with the bases loaded and Daniel Descalso followed with a single to drive in two more.
Brandon Barnes' RBI double, his second hit of the inning, made it 9-4. Encarnacion hit his 21st homer to lead off the ninth.
Rockies OF Charlie Blackmon was named the NL Player of the Week on Monday. Blackmon hit .424 with five home runs and nine RBI. He hit safely in all seven games.
Blue Jays: 1B Justin Smoak pinch-hit in the seventh after sitting out all three games against the White Sox over the weekend with a bruised and swollen left knee.
Rockies: Trevor Story was feeling better after taking a pitch off his right middle finger in Sunday's game. He took batting practice and did some throwing. He said the finger is a little swollen but improving. ... An MRI on DJ LeMahieu's left knee showed no damage and confirmed he suffered a contusion during Sunday's game against Arizona. Manager Walt Weiss said he doesn't think LeMahieu will need to go on the 15-day DL.
Blue Jays: LHP J.A. Happ (9-3, 3.42) is 3-0 in his last three starts and has averaged 6 1/3 innings in the outings.
Rockies: RHP Eddie Butler (2-4, 6.71) struggled in his last start, allowing six runs and 11 hits in five innings against Arizona.