With Derrick Favors replacing Jefferson in the starting lineup, the Jazz bolted to a 30-12 lead less than nine minutes into the game.
But Utah managed only 15 points in the fourth quarter and 16 points in the 10 minutes of overtime.
In the final 22 minutes of the game, the Jazz made only 12 of 29 shots from the field, mostly because the Raptors pushed them to the perimeter.
"We rely pretty heavily on the post game and so when we don't have that many points and that much of our offense, it's going to hurt," said Raja Bell. "… When you are missing someone of his caliber, obviously that's going to put us in a bind."
After finding little space on offense during a 1-for-9 shooting performance, Gordon Hayward agreed.
"We definitely missed him," he said. "I mean, it speaks for itself, not having him out there. He's one of our go-to guys. So we missed him, that's for sure."
Power forward Paul Millsap scored 31 points for the Jazz. Favors finished with 16.
In the second overtime, however, Toronto swarmed Millsap and the Jazz were outscored, 11-6.
Point guard Devis Harris scored all six points.
"Al is a key guy for us," coach Tyrone Corbin said. "He's a guy, when you put the ball in his hands, he does something good for us."
Corbin noted that Jefferson "takes a lot of pressure off the other bigs," a group that also includes Millsap, Favors and Enes Kanter.
"He gets us stuff close to the basket," the Jazz coach said. "Most of his shots are close to the basket instead of perimeter shots. So it's another weapon we can use and we missed him."
The Raptors' zone defense caused the Jazz noticeable trouble another result of Jefferson's absence.
"It did [hurt] because he is a little bit more experienced against a zone," Corbin said. "He and Paul read each other very well.
"Enes and Derrick aren't as experienced. They tend to stand a little bit more because it's a zone. They want to wait and wait and wait. But you have to move against it because you are getting into the 24-second clock."
A closer look
• Without Al Jefferson, the Jazz shoot 12 of 29 in the fourth quarter and two overtimes.
• Point guard Devin Harris scores all six of Utah's points in the second overtime.
• In the two overtimes, the Jazz offense stagnates. They have only one assist in 10 minutes.