It also marked the first time since 1999-2000 that the club finished in last place in the AL and the division for two consecutive years.
Tuesday's loss followed a familiar script for the Twins, as they fell behind early with Anthony Swarzak making a spot start and couldn't quite get back despite a few opportunities late in the game.
"It just wasn't enough runs for us," Twins manager Ron Gardenhire said. "Swarzak was all right, but I think he just got a little tired. We talked about 75 or 80 pitches for him, but it had been a while. Once he got to about 60, he got tired, but he made some pitches and gave us an opportunity."
Swarzak, making his fifth start of the year with Samuel Deduno missing his scheduled outing with left eye irritation, surrendered four runs on five hits over five innings.
He fared much better in relief this season, as he finishes the year with a 4.05 ERA in 73 1/3 innings as a reliever and an 8.10 ERA in 23 2/3 innings as a starter.
"I feel like there were about three innings where I was pretty good, but after that they pounded a few hits and had a few walks," said Swarzak, who was making his first start since May 25. "They had some pretty timely hitting against me. I put them in hitters' counts, and when you do that, it's usually not going to fare too well for you."
The Blue Jays got on the board first on an RBI single from Rajai Davis to score Adeiny Hechavarria, who doubled to open the third inning.
They added two more runs in the fourth on a two-run blast from Kelly Johnson before scoring again in the fifth on an RBI single from Yunel Escobar, who was thrown out trying to stretch the hit into a double.
Minnesota didn't score against right-hander Chad Jenkins until the sixth inning, when Denard Span crushed a two-run shot with nobody out. It knocked Jenkins from the game, as he gave up just those two runs on five hits over five-plus innings.
"Solid job by Jenkins tonight, I thought he pitched real well," Blue Jays manager John Farrell said. "Given that we were on a relatively short leash with him with the short rest, he did a very good job for us. Pitched ahead in the count, attacked the strike zone and put the ball on the ground."
The Twins made it a one-run game with an RBI double from Alexi Casilla with two outs in the sixth off reliever Steve Delabar. But Casilla was stranded at second base, as Eduardo Escobar grounded out to end the inning.
Minnesota had a chance again in the eighth, as Ben Revere singled with one out, but Joe Mauer flied out to center field and Revere was picked off by left-hander Darren Oliver to end the inning.
Mauer went 0-for-3 with a walk to see his batting average drop to .320. He's essentially out of the batting race, as Miguel Cabrera went 2-for-3 to improve his AL-leading batting average to .331.
"It's a little disappointing, yeah," said Mauer, who is set to establish a career high in games played with 147 on Wednesday. "But I'll go back out there and try to get some hits tomorrow."