"Great driving from Hamilton", said Sky F1's Martin Brundle of Hamilton's 66th career pole and fifth of the season. The Brit topped all three qualifying sessions, and teammate Bottas helped seal a 1-2 finish for Mercedes.
With three minutes remaining a red flag came up, halting the session, after Daniel Ricciardo clipped the wall with the left side of his Red Bull coming out of Turn 6 - prompting an expletive from the Australian driver.
"It's been hard with the tires to switch them on, it's been a struggle", Räikkönen said, who was more than a second behind Hamilton's pole time.
Engaging in a battle for pole with team-mate Valtteri Bottas as Ferrari faded, Hamilton's second and final lap following a brief red flag period would see him stop the clock at an outstanding 1min 40.593, a full half second quicker than his team and a second up on Ferrari. It was the first time we tried to go for a time in the first lap of the tyres and I couldn't get them to work as well as Lewis.
The three-time champion Austrian, who is Mercedes' non-executive chairman, also praised the team for their work in turning around a vehicle that had struggled on Friday, when Hamilton was 10th, into the fastest just 24 hours later. "Every now and then you call upon it and you don't actually extract it, but it was a flawless lap". The Spaniard won't be too anxious though, as he will start from the pit lane anyway with a 40 place grid penalty.
Vettel starts fourth but will look to benefit on Sunday.
Renault's Jolyon Palmer had barely started when his auto ground to a sudden halt on the second turn and burst into flames, leaving him in last place.
Hamilton dominated Q1 with a superb showing, as he set the fastest lap ever at the Baku City Circuit before improving on it shortly after.
Vettel will probably not have too many problems in passing his teammate, but will have to be at the top of his game if he is hoping to challenge for victory.
"With the place, with the feeling that we had, I'll happily take it and I'm not surprised with the time difference".
Force India pair Sergio Perez and Esteban Ocon finished sixth and seventh quickest respectively while Williams' Lance Stroll continued his improvement following a points finish in Canada last time out, as he qualified eighth fastest, narrowly edging out team-mate Felipe Massa.
"Obviously it's better than where I was before".
Jolyon Palmer is a man under pressure this weekend following his pointless start to the new season, and the Englishman suffered an engine failure in the opening moments of Saturday's morning running.
Alonso will start in an embarrassing 16th and Vandoorne next to last in 19th.