The three-time champion Briton steered his Mercedes to a fastest time of one minute and 11.459 seconds to outpace nearest rival and world championship leading German Sebastian Vettel of Ferrari by 0.330 seconds.
The Senna family presented Hamilton with a race worn helmet from his childhood hero.
An emotional Hamilton said: "I am shaken". The first sector was fantastic and then I managed to be just a little bit up on each one. Hamilton encouragingly got close with 1m 13.516s on the supersofts that had generally been a second slower the previous day, but when the Silver Arrows went to the softest compound with 20 minutes left he was unable to match Vettel's second-run best of 1m 12.572s, and his 1m 12.926s was also pipped by Raikkonen on 1m 12.864s.
Vettel, who leads the championship by 25 points over Hamilton, has won three races and finished second at the other three this season. He inspired me to be where I am today so to receive this is the greatest honour.
"I think we have (got the pace to win tomorrow)", Vettel said.
Vettel had a mishap on turn two on his final fast lap or he may have had a chance to nip Hamilton for the pole.
Formula One Canadian Grand Prix qualifying session 2
It got a lot better for qualifying, it felt good in Q1 and Q2. He won in Montreal in 2013 and was second previous year . He needs to make the best of it on Sunday, however.
"Nevertheless I feel the vehicle is very good, I was really happy this morning, I was happy this afternoon and it should be very good in the race so I'm looking forward to tomorrow".
Stoffel Vandoorne was 16th, 0.4s behind Alonso, while Magnussen had a delayed session and could only register a time good enough for 17th.
Pressure has been mounting on McLaren's engine partner Honda to deliver on promised improvements to the power unit but none have been ready for Montreal and the team continues to languish down the timesheets.
Local favorite Lance Stroll, who would be the first native Montrealais to drive in the Canadian GP since Jacques Villeneuve, the 1997 world champion and the son of the track's namesake, was 17th.
But he will be starting 17th and will need to produce something extra special to crack the top 10.
Hamilton was seventh in Monaco in the last race, his lowest finish this year and his second time missing the podium in six races.
Williams' Felipe Massa was seventh, his team-mate Lance Stroll struggling so far on his debut at his home race with the 18th fastest time, almost a second behind the Brazilian.
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