The cruiser collided with the vehicle near the intersection of Midland Avenue and Lawrence Avenue East at around 12:40 p.m. Thursday.
The cruiser was one of three travelling along Midland Avenue with lights and sirens on and trying to navigate around vehicles that weren't pulling over, witnesses said.
"The one cop went to merge into oncoming traffic, I guess to get around. And there was a lady there and they hit head on. And it was the loudest bang you've ever heard," said Jeffrey Regular, who witnessed the crash.
"Never seen an accident like that before in my life."
The debris of the cruiser was scattered in a wide radius from the site of the crash scene.
The officer was trapped in his vehicle for about 15 minutes before being extricated. An Ornge air ambulance was called to the scene, but he was ultimately taken to hospital in an ambulance.
Following the crash, Midland Avenue was closed between Ellesmere Road and Lawrence Avenue East in both directions.
The Special Investigations Unit, which probes any incidents involving police that resulted in death or serious injuries, is now investigating the crash.
A news release the SIU issued on Thursday afternoon said that both the injured officer and the 57-year-old woman were taken to Sunnybrook Health Sciences Centre for treatment of their injuries.
The SIU said the police car was headed south on Midland Avenue at the time of the collision, while the civilian vehicle was driving north.
Three SIU investigators, two forensic investigators and a collision reconstruction expert are now probing the circumstances of the crash.
With files from @jlancastercbcSuggest a correction