The teenager was pulled from the water and taken to the trauma unit of Sunnybrook Hospital in critical condition. Police say he was submerged for almost 30 minutes.
"It took a little while to get down to the person still in the car, but we managed to get him out and he's still in trauma being worked on," Toronto Sgt. Lawrence Zimmerman told reporters at the scene.
The teenager died in hospital at 10:32 p.m.
The other four occupants, all of whom were also 16 years of age, were either uninjured or had minor injuries, Toronto Traffic Services said.
The vehicle crashed through a handrail and plunged into the water near Lakeshore Road and Don Roadway. The call came in at about 5:30 p.m., and all five had to be rescued from the water, Toronto fire officials say.
Toronto Fire says it's too early to tell how the vehicle ended up in the water. Investigators are looking at whether speed was a factor.