Dillon Wamsley kicked a 39-yard field goal on the Gaels' first possession of overtime to put his team up by three. Guelph needed at least a field goal to keep the extra period going, but Fortino broke a tackle after the catch and crossed the goal-line before being mobbed by teammates.
Guelph will play the winner of the other OUA semifinal between No. 1 McMaster and No. 8 Western that took place later Saturday in the Yates Cup next weekend.
Trailing 36-14 with just over 10 minutes to go in the fourth, Guelph started on the comeback trail when Jake Reinhart returned a fumble 15 yards for a touchdown.
Lindsey then broke for an 80-yard TD run with under four minutes to play. Backup quarterback Lucas Nangle entered the game with 44 seconds left and found Saxon Lindsey to make the score 36-34. Carl Trivieri then caught the two-point conversion to force overtime.
Jazz Lindsey finished the day 14-of-36 passing for 198 yards, two touchdowns and an interception. He also had 99 yards rushing and a TD.
Fortino was the top receiver for Guelph, hauling four catches for 86 yards and a TD.
Elsewhere in CIS playoff action it was: No. 2 Laval 46, McGill 9; No. 10 Sherbrooke 42, No. 3 Montreal 24; and Saint Mary's 49, Mount Allison 11.
No. 3 Calgary welcomed Manitoba in the Canada West semifinal later Saturday. The winner of that one will play No. 7 Regina in the Hardy Cup next weekend.
At Guelph, Ont., Queen's quarterback Billy McPhee was 22-of-33 passing for 226 yards and touchdown but threw three costly interceptions.
Jesse Andrews had a big game on the ground for the Gaels, rushing for 117 yards and two touchdowns on 27 carriers. T.J. Chase-Dunawa added a 34-yard punt return for TD.
Justin Chapdelaine caught five passes for 79 yards, while Giovanni Aprile also hauled in five catches for 72 yards and TD.
Leading 24-14 at halftime, Queen's scored 12 points in the third quarter on a safety, a Wamsley field goal and Andrews' second TD of the game to lead 36-14 heading to the fourth before collapsing in the final period.
No. 2 Rouge et Or 46, Redmen 9
At Quebec City, Tristan Grenon threw for 342 yards and two touchdowns as Laval hammered McGill to advance to next weekend's Dunsmore Cup.
No. 10 Vert et Or 42, No. 4 Carabins 24
At Montreal, Sherbrooke stunned the Carabins to advance to the Dunsmore Cup, where the Vert et Or will take on Laval.
Huskies 49, Mounties 11
At Halifax, Jean Legault threw two touchdown passes to Kevin Wuthrich and another to Carl Fitzgerald as Saint Mary's thumped Mount Allison.
The Huskies will play at Acadia next weekend in the Loney Bowl.