Tommy Tremblay scored twice for the Patriotes (1-0), who will face the UNB Varsity Reds (1-0) on Saturday with the winner advancing to Sunday's University Cup final.
The loss ends the season for the tournament host Huskies (0-2), who fell 3-1 to UNB on Thursday.
"I'm so proud of my players. We just beat a very good hockey team on their home ice, in a very challenging environment," said first-year UQTR head coach Gilles Bouchard. "We're not out of the woods yet. We have to face another formidable opponent tomorrow night."
Earlier, the Alberta Golden Bears beat the Saint Mary's Huskies 4-3.
UQTR opened the scoring six minutes 21 seconds into the game. After skating out from behind the net, all-Canadian forward Felix Petit saw his shot blocked by a defenceman but the puck rebounded straight to the stick of Tremblay, who fired into an empty net.
"Getting that first goal early in the game was key for us," Tremblay said. "We hadn't played in six days, had a long travel, and we've only had two practices since we got here. We were a little nervous at the start of the game, so after that first goal, we relaxed a bit."
Saskatchewan tied it with 3:21 left in the first period during a four-on-three power play. At the end of a mad scramble in front of the Patriotes' net, Kyle Bortis pushed the puck past goaltender Marc-Antoine Gelinas, who had already made two saves on the sequence.
Saskatchewan held a 13-12 edge in shots on goal after 20 minutes.
Following a scoreless second period, Donovan, a fourth-year centre from Gatineau, Que., broke the deadlock 1:11 into the third with a blast from the point that eluded Ryan Holfeld on the glove side.
Tremblay, a sophomore from La Tuque, Que., rounded out the scoring in an empty net with 0.1 second left on the clock.
The Patriotes outshot the Huskies 35-25.
"It's disappointing for sure. It's not the result we were hoping for at this championship, but it's not for lack of effort," said Saskatchewan coach Dave Adolph. "We dug ourselves a hole with yesterday's two-goal loss and tonight, we just couldn't get anything going offensively. Hats off to UQTR. They played very well."
In the other game, Levko Koper scored 2:51 into overtime as the Golden Bears stayed alive with a win over Saint Mary's.
The top-seeded Golden Bears (1-1) were facing a must-win situation in their second and final preliminary round contest after dropping their opener 2-1 to Waterloo on Thursday.
Alberta can still advance to Sunday's gold-medal game if Saint Mary's beats the Warriors by a 1-0 or 2-1 score on Saturday. The Huskies (0-1) get to play for the University Cup if they win by any other score.
"We'll worry about the various scenarios in a few hours. We get to live another day, and for now it’s all that matters," said first-year Alberta coach Ian Herbers. "I thought we had lots of energy in the early goings but, like yesterday, we couldn't buy a goal."
After outshooting Waterloo 43-13 on Thursday, the Canada West champions doubled Saint Mary's 40-20 in their second outing, including 17-5 in the opening period, which ended 1-1.
"It's pretty simple. We only win 1-0 or 2-1 tomorrow and we go home," said Huskies coach Trevor Stienburg. "This is nothing new for us. We've battled and overcame adversity all year. This is just another challenge. The guys will be ready."