Two-time world champion Fernando Alonso of Ferrari maintained his improvement by topping the times with a best lap of one minute and 15.205 seconds, ahead of Championship leader Sebastain Vettel.
Japanese Kamui Kobayashi had crashed heavily in Friday afternoon's second free practice session for the Canadian Grand Prix causing the session to be red-flagged to a halt.
The 24-year-old Sauber driver lost control of his car at the 125 kph turn four on the Circuit Gilles Villeneuve and crashed sideways into a trackside wall.
He was unhurt, but was assisted away from his accident by the medical crew.
It was the second time the day's practice had been halted for a red flag and the third big accident.
World champion Sebastian Vettel walked away unhurt from a crash in the morning and Adrian Sutil of Force India crashed earlier in the afternoon.
Vettel's collision with the 'wall of champions' at the final chicane in his Red Bull brought the morning session to a halt.
For Sauber, Kobayashi's collision with the barriers continued a bad day after Mexican rookie Sergio Perez, his Sauber team-mate, had pulled out due to feeling unwell, two weeks after his high-speed crash at the Monaco Grand Prix.
In his accident this time, Kobayashi turned his car into the chicane made up of turns three and four, but was too aggressive on the kerbs. His car lifted up and flew almost directly across the circuit into the wall.
No sooner had the session been re-started, than the afternoon action was stopped by the third red flag of the day when Belgian Jerome D'ambrosio lost control of his Virgin car and smashed into the barriers.
He was also unhurt and walked back to the pit lane.