The downpour flooded underpasses, trapping people in their vehicles with water reported as high as the windows, the Canadian Broadcasting Corp. reported.
Officials said nearly four inches of rain fell Monday evening, knocking out power to more than 335,000 customers.
Hydro One said of the approximately 300,000 customers affected, only 30,000 to 40,000 had their power restored as of midnight because of "significant flooding" at two of its transmission stations, the CBC said.
Toronto Hydro said about 35,000 of its customers were without electricity early Tuesday and could not estimate when power would be restored completely.
About 1,400 people were caught by flooding aboard a northbound commuter train. Officials said it took police and firefighters about seven hours to ferry everyone to safety aboard small inflatable boats.
Authorities say five or six of the trapped commuters were treated for minor injuries.
Transit officials said some of the track was "completely under water."
Little India resident Kurt Krausewipz told the Toronto Star the "thick heavy sheets of rain" reminded him of monsoon season in Southeast Asia.
The few hours of heavy downpour was "one of the wettest moments in Toronto's history," Environment Canada senior climatologist Dave Phillips said.
Since June 1, downtown Toronto has seen nearly 6 1/2 inches, of rain, about double the usual amount, the Star said.
"We've had a month worth of rain [on Monday]," Phillips said.