Hamilton, a six-time Canadian Grand Prix victor, was nowhere, in fifth place.
"It feels great to be back in France".
Hamilton, a point behind Ferrari's Sebastian Vettel after seven races, complained about his car's handling over the radio in the first session but still put in a best time of one minute 32.231 seconds.
Hamilton, however, believed the stewards were too lenient on Vettel for the collision.
Red Bull's Max Verstappen, who finished as the runner-up to Hamilton, has courted criticism this season following a number of crashes.
Bottas said: "It wasn't a bad lap, not flawless either". We can be happy with third for tomorrow (though).
Take a look through the gallery above to see the latest Drivers' Championship standings after the French Grand Prix.
On an initially dry track following heavy rainstorms, which had curtailed final free practice, the air temperature was 22 degrees Celsius and the track 30 when qualifying began.
Orlinski's work was also exhibited at the Circuit Paul Ricard where the race was held, his style recognisable from the trophies given out.
Alonso won the 24 Hours of Le Mans last weekend but failed to progress from Q1 and will start 16th, while Stoffel Vandoorne is back in 18th.
Hamilton's pace maintained Mercedes supremacy in every session from Friday morning, but as the rain intensified in Q2 he was struggling for comfort in his vehicle.
The stewards awarded Vettel a five-second penalty, but the penalty had little impact on the race after the Ferrari driver managed to build up a substantial gap over Bottas - who had been nursing floor damage, and the rest of the field.
Ferrari responded by going out on ultra-softs -- Mercedes were on super-softs -- and Vettel jumped to second, Raikkonen to third as the rain relented and the track became faster in the final dramatic minutes of Q2.
Hamilton s Mercedes team-mate Valtteri Bottas, who was second in opening practice, was hit by a water leak in the afternoon and wound up seventh after being prevented from completing the second session.
A wheel then came off Sergio Perez's Force India vehicle at speed on the Mistral straight in the late afternoon.