Six days after their wheel-banging duel in Texas, where Hamilton won the United States Grand Prix to clinch the title, Rosberg secured his fourth consecutive pole by 0.188sec as Mercedes claimed their 13th front row lockout this year.
It was the 20th pole of Rosberg's career and continued to leave Hamilton frustrated as the Englishman seeks his 50th pole position. Hamilton has not started from pole since the Italian Grand Prix in early September.
Rosberg clocked a best lap of one minute and 19.480 seconds to outpace Hamilton by 0.188 seconds.
"Angry..." he said, referring to the 30-year-old German's tetchy reaction to being pushed off-track by Hamilton on the opening lap last weekend.
That failure to exploit pole and win represented another failure in Rosberg's current travails as he seeks to improve on just two wins from his last 10 pole positions.
With 20 poles, Rosberg has the most by any driver not to have won a world title.
"I have felt good all weekend and been fast here," he said.
It's very good to start from pole and there is a very long run down to Turn One and I am sure we have a good 'race' car so it should be interesting, an interesting battle!"
"There were a couple of moments when the car felt spectacular, but there are a few places where I can improve - my driving and my set-up. Nico has been very fast,"" said the world champion.
He starts ahead of Sebastian Vettel of Ferrari and the two Red Bulls of Daniil Kvyat and Australian Daniel Ricciardo.
Vettel said: "It's a fun track to drive on and it should be a good race. The Mercedes were just too quick for me today."
Valtteri Bottas was sixth ahead of his Williams team-mate Felipe Massa, Dutch teenager Max Verstappen of Toro Rosso, local hero Mexican Sergio Perez and his Force India team-mate Nico Hulkenberg.
The biggest roar, predictably, came for Perez, who had a photograph of the Pope in his Force India car.
Sadly for Jenson Button, a recurring problem with his McLaren's Honda engine forced him to miss qualifying.
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