Trailing by 19 points at halftime, Calgary rallied with four touchdowns and a pair of two-point converts to remain atop both the CFL and West Division standings at 10-1.
Stampeder quarterback Bo Levi Mitchell threw for 198 yards and a pair of touchdowns, but he went down awkwardly on his left leg in the fourth quarter when he was tackled on a four-yard run.
Mitchell left the game with just over six minutes remaining and there was no immediate word on his status following the game.
Down eight points when Mitchell went out, backup Drew Tate finished the drive and tied the game with a 15-yard touchdown throw to Jabari Arthur and a two-point convert toss to running back Jon Cornish at 9:53.
Cornish scored the winning touchdown and his second of the game on a 30-yard catch-and-run at 13:12. On their final drive, Toronto turned the ball over on a fumble by quarterback Ricky Ray with nine seconds left.
"It's victories like this that really show you how good you can be," Cornish said. "This is a win, but if we can do things like this in playoffs, that's what really matters. This was a key learning experience for us."
Mitchell threw touchdown passes to Sederrik Cunningham and Brad Sinopoli before he was injured.
Saskatchewan Roughriders quarterback Darian Durant is expected to miss the rest of the regular season because of an elbow injury suffered last week. Travis Lulay of the B.C. Lions went on the six-game injured list last week with a dislocated shoulder.
Calgary's Matt Walter scored a two-point convert on a two-yard dash. Stampeder kicker Rene Paredes kicked a 28-yard field goal and Toronto kicker Swayze Waters was good on a 36-yard attempt in front of an announced 28,607 at McMahon Stadium.
Ray made touchdown throws to Spencer Watt, Jason Barnes, Trent Guy and Andre Durie. Ray totalled over 300 passing yards in a game for the first time since July 5.
The Argos lost momentum, however, because of 128 yards in penalties and three turnovers.
"That's what we've been fighting with all year, penalties and turnovers," Ray said. "Those were our biggest mistakes tonight again. It's hard to beat anybody in this league when you're doing that let alone the best team in the league.
"Until we get those two areas cleaned up it's going to be like this, a fight to win football games."
The Argos dropped to 3-8, but remained tied for the East Division lead with the Montreal Alouettes, who lost to Edmonton on Friday.
Cornish rushed for 174 yards in the game, including a 79-yard scoring rumble in the third quarter.
The CFL's Most Outstanding Player in 2013 missed six games in July and August with concussion symptoms. Cornish has rushed for a total of 694 yards in four games since his return.
"Jon Cornish is a force," said Stampeders head coach John Hufnagel. "We know that. We want to get him the ball and he did some damage out there."
The victory was costly for Calgary because not only Mitchell was unable to finish the game. Defensive end Ben D'Aguilar and receiver Marquay McDaniel went out in the first quarter.
The defensive line was further decimated when end Charleston Hughes and tackle Demonte Bolden left the game in the second half.
"Not quite sure," Hufnagel said when asked of their status. "All those guys are getting MRI's and we'll find out tomorrow."
Argos receiver Chad Owens, the CFL's MOP two years ago, didn't play in Calgary because of a leg injury. He's expected back in the lineup Friday against the B.C. Lions in Vancouver. Durie played Saturday after missing eight games with a broken collarbone.
The Stampeders have won nine in a row versus East Division clubs and face the Alouettes in Montreal next Sunday. The Argos will practise in Calgary until Thursday when they depart for Vancouver.