"It is really, probably the most intense, wettest moment in Toronto's history," Environment Canada senior climatologist David Philips said.
Phillips said two separate storm cells moved over the city at the same time, and then stalled over Toronto for hours.
"It's almost like Toronto was a target with a bull's eye," he said.
Pearson International Airport reported 12.6 centimeters (4.96 inches) of rain throughout Monday, breaking the previous single-day rainfall record for the city set back on Oct. 15, 1954, when Hurricane Hazel dumped 121 millimeters (4.76 inches) of rain.
The downpour left several roads and underpasses under water, forcing some people to abandon their vehicles. Subway, bus and streetcar services were either halted or slowed to a crawl, creating chaos during the evening rush hour. Many finally arrived home hours late to deal with flooded basements and leaking windows in residences which had lost power.
In one of the more serious incidents, 1,400 people were stranded on a northbound commuter train as murky water seeped into the cars. It took police and firefighters about seven hours to ferry everyone to dry ground aboard small inflatable boats.
Toronto authorities warned it would take some time for everything to return to normal, but praised city crews for their work.
"Toronto has persevered we have weathered the storm," Mayor Rob Ford said at city hall. "At some points it was really scary out there. I saw a few people panicking."
About 70,000 customers were without electricity Tuesday night, 25,000 due to rolling blackouts. About 300,000 customers had been left in the dark at the height of the outage Monday due to "significant flooding" at two transmission stations.
One of the transmission stations remained under about six to nine meters (20 to 29.5 feet) of water, said Toronto Hydro CEO Anthony Haines. He said the utility hoped to restore power by Wednesday morning.
Toronto's flash flooding comes two weeks after extensive flooding in Calgary turned parts of the western Canadian city into a lake and forced up to 100,000 Albertans from their homes. Three bodies were recovered during the floods.