Further back, Ferrari's Charles Leclerc came in third to join Hamilton and Vettel on the tense podium, while Valtteri Bottas came in fourth to round off a dominating afternoon for the top two teams.
Vettel stopped Mercedes' sequence of four front-row lockouts with his first pole since July 2018, a run of 17 races, with a final lap hailed as "outstanding" by Sky F1's Martin Brundle.
The second practice run was very different from the first, when Mercedes easily set the fastest lap times and dominated the field.
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Keanu Reeves Revealed As Star Of ‘Cyberpunk 2077’ At E3 2019
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Rookie Norris, 19, took umbrage with his compatriot's remarks on the eve of Sunday's Canadian Grand Prix, believing them to be a jibe directed at him, and his fellow British novice George Russell, 21. Tune in to ABC at 2:10 p.m. ET for the live broadcast of the race from Circuit Gilles Villeneuve to find out.
'I hope the people come back because they are the reason we put on this show and drive these incredible cars, it is just a shame'.
"Hard to crack", Vettel said of Hamilton.
"I'm glad I've been able to split the Ferraris today and tomorrow is going to be an interesting race".
"Very happy for the team because the last weeks have been quite tough for us".
The defending champion Vettel of Germany snatched pole position from reigning world champ Lewis Hamilton of Mercedes in the dying moments of the qualifying session.
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Vettel then leapt to Hamilton's defence, urging the fans to direct their annoyance at the decision, and not at Lewis for collecting the win.
The stewards document, which was issued by the FIA shortly after the race, also reminded Ferrari of its right to appeal "certain decisions" under Article 15 of the FIA International Sporting Code and Article 9.1.1 of the FIA Judicial and Disciplinary Rules. "But our vehicle is a lot better this year in the slower and medium-speed corners".
As for Stroll, his immediate goal will be to emerge from Q1 - the first round of qualifying - on Saturday, something he has failed to do in the last 10 tries dating to last season.
Mercedes had the added concern of one of its customer engines - in the back of Lance Stroll's Racing Point - blowing up in the final practice session before qualifying.
Magnussen's crash prevented a number of drivers from posting a quick lap time at the end of Q2, most notably Red Bull's Max Verstappen. He is looking for his seventh victory in Montreal, which would tie Michael Schumacher's record.
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Treasury Secretary Steven Mnuchin says he held a constructive meeting with the head of China's central bank and that their discussion on trade issues was "candid".