Championship leader Rosberg produced a near-flawless lap of controlled speed around the barrier-lined Circuit Gilles Villeneuve to outpace his nearest championship rival by just 0.079 seconds in the final seconds of a dramatic qualifying session on Saturday.
Two weeks after his controversial pole success at the Monaco Grand Prix, the German erased all doubts about his raw speed and talent as he drove with precision and pace to secure his first pole in Canada, his second pole in succession and the seventh of his career.
"I know it's a track where Lewis is really strong," said Rosberg. "I'm very happy it worked out. It has been a fantastic day and through the weekend we have been progressing all the time and I'm in the best position for tomorrow so I am very happy."
Asked how he achieved his success against Hamilton on one of the Briton's favourite tracks, he added: "It's just working at it all the time, looking at the data, working with engineers and trying to understand areas where I can do better. It's just a process and I'm glad it's worked out."
"But it's a great to get a one-two for the team and a fantastic performance. Let's hope we can make history tomorrow."
Defending four-time world champion Sebastian Vettel bounced back from an inconsistent weekend to grab third place in his Red Bull car ahead of Valtteri Bottas and his Williams team-mate Felipe Massa.