The longtime NBA executive confirmed that he had been relieved of his duties.
"In my 18 months in Canada I came to love the city of Toronto, world-class city with terrific basketball fans," Stefanski said in a text message to The Canadian Press. "I wish the team only the best."
Stefanski's departure follows a shakeup in the Raptors' front office.
Longtime general manager Bryan Colangelo was relieved of his GM duties on May 21, although he remains the team's president.
Colangelo was replaced by Masai Ujiri as Toronto's GM on May 31.
Another Raptors official confirmed that other members of the team's front office had been fired on Sunday.