Hamilton further improved on his best mark early in the session early on before donning the super soft compound for the first time and going quicker still.
McLaren team-mate Jenson Button endured a miserable day, however, and was forced to sit out the majority of the session as his McLaren team worked frantically to fix an oil leak on his gearbox that curtailed his running in FP1.
Despite the forecast of rain, the weather stayed clear in a session that saw no shortage of on-track incident on an already greasy track.
Timo Glock spun his Marussia in a dangerous position into turn 1 before Fernando Alonso got it all wrong into turn 8, spinning his Ferrari 360 degrees but just managing to keep it out of the barriers after coasting over the grass.
Hamilton then came perilously close to collecting a Ferrari mechanic on his way into the pits after Pedro de la Rosa had managed to do just that to one of his own crew in the morning, sending the unfortunate employee to hospital for a scan.
And after Heikki Kovalainen’s accident caused FP1 to be red flagged, Bruno Senna repeated the feat in the afternoon, losing control of his Williams into the final corner and smashing into the Wall of Champions.
But while Kovalainen’s mechanics did a superb job to repair his car for the second session, it signalled the end of Senna’s day.
"It was a big shunt. I was a bit frustrated being held up by traffic and pushed a bit hard into the chicane," said Senna. "They have plenty of spares so I expect to be back in action tomorrow."
Button finally managed to get some meaningful running with just under 20 minutes of the session remaining but complained of a lack of front end grip on the yellow soft compound tyre before switching to the super softs. He managed a best mark of 1:15.812 to finish the day ninth quickest but could have been running with a heavy fuel load for race simulation.
But the day belonged to Hamilton, whose McLaren seemed perfectly dialled into the notoriously tricky Circuit Gilles Villeneuve. Not only did he consistently lap quicker than his rivals, he also completed more laps than any other driver, gathering vital data for his pit crew ahead of the weekend.