The highway was closed in both directions from the south end at the Gardiner Expressway north to Bloor Street at about 5 am, causing major traffic problems for the commute.
Officials say the Don River overflowed its banks, sending water onto the highway.
"This area is habitually a flooding area because of the design of the Don Valley, it is low in this area," said Constable Clint Stibbe with the Toronto Police. He said this was actually the worst flooding he had ever seen on the DVP.
Tow trucks were called to the scene, helping vehicles and motorists who were left stranded on the flooded roads. Water fully submerged the highway creating a barrier between the north and southbound lanes.
According to Environment Canada, between 60-70 mm of rain was recorded in parts of Toronto as of 8 am.
Some GO Transit trains on the Richmond Hill line were also affected during the morning commute.
A very moist air mass from the American Midwest created favourable conditions for the development of thunderstorms and heavy downpours Tuesday and early Wednesday.
Several rounds of storms affected parts of southern Ontario through the overnight hours, bringing strong winds, frequent lightning and heavy rain to the region.
"I honestly don't remember the last time I've seen it rain this hard," Tweeted a Weather Network viewer from Waterloo.
In Brampton, there are unconfirmed reports of a small tornado or a micro-burst. Downed trees and branches fell onto homes and roads in the area.
Environment Canada is sending a surveyor to the area to investigate.
"Rainfall warnings that were in place for the City of Toronto and parts of the GTA were dropped by 6 am on Wednesday and the rain should gradually taper through the morning," says Gerald Cheng, a meteorologist at The Weather Network. "Sunny breaks and rising humidity throughout the day however, could help to fuel more thunderstorms across the region."
According to Environment Canada, there is a risk for isolated thunderstorms over southern and eastern Ontario on Wednesday, with a slight risk that some of these storms may be severe, especially near the lower Great Lakes and St. Lawrence Valley.
Torrential downpours, damaging winds and hail are the main threats with these storms.
With files from The Canadian Press