Hydro One said that of about 300,000 people affected, only about 30,000-40,000 had their power restored as of midnight ET due to "significant flooding" at two of its transmission stations.
Toronto Hydro said about 35,000 of its customers were still without electricity as of about 3 a.m., primarily in the west end of the city. The utility could not say when it expected full power to be restored.
The CBC's meteorologist Jay Scotland said a heavy downpour had been forecast, but the rain was "unprecedented" with 126 millimetres falling across Toronto — most falling during the evening commute.
"That even topped Hurricane Hazel's one day rainfall total going back to 1954," said Scotland, noting that the amount that fell then was 121.4 millimetres.
The rain left underpasses and many basements flooded and a number of people trapped in vehicles — some with water up to their vehicle windows.
About 1,000 people were caught by the flooding aboard a northbound GO Transit train, and it took police and firefighters about seven hours to ferry everyone to dry ground aboard small inflatable boats.The operation ended at about 12:30 a.m. Authorities said five or six people were treated at the scene for minor injuries.
Go Transit said the storm left portions of track "completely under water" on its Milton, Richmond Hill and Lakeshore West lines and suggested passengers seek alternative ways to travel Tuesday morning.
This morning, a commuter reported that shuttle buses were being used on the Lakeshore West GO Train line between Port Credit and Long Branch to move passengers past a flooded area.
Toronto police Const. Wendy Drummond said she's never seen a flooding incident this severe in the city, but emergency crews were prepared to respond.
"Somebody looking at the scene may not understand everything that is happening, but rest assured that efforts, emergency response efforts, have been in the planning stages from the very onset," she said.
Two people attempted to flee by jumping out the train and swimming to shore. Rescuers had to pluck one of them from the murky water.
Toronto Transit Commission Chair Karen Stintz recommended the public move slow and steady today, treating it as a "summer snow day."
"If you can somehow avoid the commute, please do. Big cleanup in progress," Stintz tweeted.
Extra TTC staff were on site this morning at Jane station in the city's west end, where a major stretch of the east-west subway line was shut down due to heavy flooding at Kipling station.
As many as 70 buses were going back and forth between Jane and Kipling, helping to move the thousands of commuters who use the line every day.
The CBC's Trevor Dunn said Jane station was busy, with some confusion, but that shuttle buses were running continually.
The TTC worked through the night to repair the damage at Kipling, but there was simply too much water in the underground station.