Ricciardo meanwhile overtook Raikkonen off the line and settled in behind Hamilton.
Red Bull chief engineer Paul Monaghan admitted the MGU-K from Monaco is unlikely to be re-usable.
Verstappen, who started from the rear of grid at the Monaco Grand Prix after a crash in qualifying, offered the promise of something much better in Montreal, taking full advantage of an upgraded power unit to clock a polished one minute, 13.302 seconds around the 2.7 mile (4.34 km) sun-splashed Circuit Gilles Villeneuve.
"We did not have the smoothest day".
Valtteri Bottas' Mercedes will also start in the front row, coming in about one-tenth of a second slower than Vettel. In the first practice, the team Red Bull found a fault in the engine, so in the second session for a long time the Australian auto was demolished.
"I am not happy with sixth, but am I happy with the way I drove and actually what we did, yes". He sits sixth in the standings some 75 points behind leader Lewis Hamilton and with less than half the number of his Australian Red Bull team-mate Daniel Ricciardo.
Kiwi driver Brendon Hartley, whose F1 future is up in the air after it emerged the Toro Rosso team made a bid for McLaren protege Lando Norris, was 12th and 1.691s off the pace in the second practice.
The young Dutchman clocked the best time of the day in the afternoon session, one minute, 12.198 seconds, ahead of Ferrari's Kimi Raikkonen and Red Bull team mate and Monaco Grand Prix victor Daniel Ricciardo. "If we got in that mess around here on this circuit, it is not as bad as Monaco but it is still very hard to make much progress here".
But after the dreary spectacle in Monaco a fortnight ago, at least we can rely on one of the finest overtakers in the sport fighting his way back through the field to provide the entertainment this weekend. His best lap was the slowest in the field at 1:17.145, but he was there just to get the feel of an F1 vehicle and help the team test it on two types of tires. "If we can escape this weekend without it, I'd rather take it somewhere else". And having such good momentum at the moment I think a penalty would take a bit of wind out of our sails.
"I think so", he said with a laugh. "The vehicle was working really well". "So it sets us up to be aggressive in attack, so should hopefully make for some good TV as well".
"If the others are sliding around in dirty air or whatever, we should be able to get a bit more out of them". Fortunately the forecast looks good this year, with only partly cloudy skies predicted for both Saturday's qualifying and Sunday's race.