Edwin Encarnacion laced a line-drive game- field line in the 12th inning to lift the 3, hampering Los Angeles' chances of reaching the postseason.
The Angels fell three games behind the AL wild-card leading Boston Red Sox, who were idle on Thursday. The Angels dropped a game behind the Tampa Bay Rays, who defeated the New York Yankees, 15-8, Thursday.
"They know what the stakes are," Angels manager Mike Scioscia said. "They know they not only have to play well, but we have to also finish games off and we have to win. There's not a motivation problem with the guys in that room. They understand and they're playing hard."
Jose Bautista had three hits with an RBI and run scored while Eric Thames added two hits, including a home run for the Blue Jays, who are now 11-0 in extra inning games this season. They've won three of their last five.
Toronto rookie Henderson Alvarez threw seven solid innings, allowing three runs on seven hits while striking out four.
Garrett Richards (0-2) surrendered the game-winner to Encarnacion, who smacked a 3-2 offering for his 17th homer of the year.
"A walk-off, I don't care what time of the year it is, it's always exciting," Blue Jays manager John Farrell said.
Ervin Santana worked six-plus innings of two-run ball for the Angels. He scattered six hits while walking five and fanning five.
Alberto Callaspo launched a solo shot into the right field seats in the second to put the Angels on the board.
In the home-half of the fifth, Thames laced a one-out double to left and Bautista followed by tying the game with a base-hit to center field.
Erick Aybar lead-off the sixth with a single and Howie Kendrick slapped one in the right-center field gap for a triple. Two batters later, Torii Hunter grounded out to shortstop to score Kendrick, who went on contact for a 3-1 lead.
Thames chased Santana out of the game in the seventh with a solo home run to right field to trim the Angels advantage to 3-2. Bobby Cassevah came on for Santana and walked Bautista. In a wild play, Adam Lind smoked a sharp groundball which deflected off of the glove of first baseman Mark Trumbo into short center field. Lind tried to turn the single into a double, but was thrown out at second. Cassevah threw a wild-pitch in the dirt with Encarnacion at the plate to bring Bautista in from third to tie the game.
The Angels come home to play the final six games of the season. They begin a three-game series against Oakland on Friday, and close the year against the first-place Rangers, whose magic number to clinch the division is two. They finished 41-40 on the road this season.
Blue Jay rookies have hit 46 home runs this season...Toronto finishes the year 42-39 at home...It was the 13th walk-off win for Toronto and the 13th walk-off loss for the Angels.