Four-time world champion Hamilton has had six poles and six wins overall in Canada and arrived seeking a record-equalling seventh victory.
"I was a bit confused". I think we need a little bit of time to understand the full picture but as I said I'm not yet happy with the auto.
"Some of the marshals were already celebrating", he said.
"You can see just how tight things are at the front of the grid, so I think it could be tricky to overtake tomorrow".
Vettel picked up his second career victory at the Circuit Gilles Villeneuve and the first for Ferrari in Montreal since Michael Schumacher won three in a row from 2002-04.
This left Vettel and Bottas out in front, 24 seconds ahead of Verstappen, but still running on their original ultra-softs.
Max Verstappen took third place in qualifying with Hamilton fourth quickest with a lap of 1m 10.996s.
Vettel's best lap time of one minute 10.776 seconds bested the record of 1:11.459 set past year by Mercedes ace Lewis Hamilton.
"It will be interesting to see how it does in the start of the race, especially because Red Bull will start on the HyperSoft. You can't come to Montreal and think it's going to be a walk in the park because that's the kind of wake-up call you get".More news: Samsung Galaxy A6, A6+ now available
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"Everybody needs to assess how to improve performance in order to optimise on those marginal gains because those marginal gains are going to make all the difference".
Behind the leaders, there was chaos when Williams's Canadian Lance Stroll squeezed Toro Rosso's Brendon Hartley into the wall.
On the restart, Sergio Perez skidded onto the grass but managed to straighten himself out and rejoin the race. He had lost two seconds and Vettel, turning the screw, responded with a fastest lap before cruising to a crushing victory. She joins Pele in the hall of F1 flag gaffes, as the football legend forgot to wave it at all when he was supposed to at the end of the 2002 Brazilian Grand Prix. "I quickly saw that it was going to be hard to take pole position but you always do your best and try to get the best out of the vehicle". He earned his first Formula One points with a ninth-place finish at Circuit Gilles Villeneuve past year.
Valtteri Bottas was second in his Mercedes, about six seconds back.
Mercedes said they had detected a fault making the auto run hot in the opening stint and added cooling at an early pitstop to help the situation.
"It's not one factor or the other, but every piece of the puzzle that we need to get right if we want to win". There's been many occasions it's been close.
"But at the moment they are doing as well as we are".
"Lewis made a useful improvement on that last run but was never totally comfortable on the HyperSoft tyre today and his qualifying position shows that".
In the closing runs of Q2, Red Bull's Daniel Ricciardo set a then lap record of 1m 11.434s around the Circuit Gilles Villeneuve.