Defoe was to undergo a scan Sunday for a possible sports hernia.
The 31-year-old England forward had scored 11 of Toronto's 27 goals going into Saturday's game.
A team spokesman said the club wasn't sure when the problem first showed up, but it could have happened last Wednesday in a game against D.C. United.
Defoe arrived in January in a transfer from England's Tottenham. He is one of Major League Soccer's marquee players with a salary of US$6.18 million this season.
Defoe was due to play in the MLS all-star game Wednesday against Bayern Munich in Portland.