Vettel will start the season-ending race in fourth place, a position good enough to secure his third title in a row if he keeps it in what promises to be a rain-lashed race at Interlagos on Sunday.
The 25-year-old German is sure to move up a place soon enough in the race, with Australian team mate Mark Webber starting alongside in third place and in no doubt about what he will be expected to do.
"All in all we are in good shape and we have been competitive and we will see what we can do tomorrow," said Vettel, who made a mistake on his first run in the final session.
Alonso, 13 points adrift of Vettel, has to finish on the podium to have any hope of taking his third title and the Spaniard gave himself a mountain to climb with eighth place on the starting grid.
He could move up a place, however, with Venezuelan Pastor Maldonado qualifying sixth but set to face the stewards after missing a weighbridge in the second phase of qualifying.
Alonso can also count on the support of his Brazilian team mate Felipe Massa, who qualified fifth at his home circuit but is sure to let the title contender go past when the opportunity arises.
"Ninth in USA and eighth here so more or less as I expected," Alonso told reporters. "I will try to achieve the podiums which we achieved in Abu Dhabi and Austin from those positions."
Hamilton's pole, the 26th of his career, was McLaren's first in Brazil since Mika Hakkinen in 2000 and the Briton will start next to Jenson Button in the team's 62nd front-row lockout.
"I think the weather will be tricky tomorrow, it will make it more of a lottery," said Hamilton, who is moving to Mercedes next season after what will be an emotional farewell to a team that has been part of his life since he was 13 years old.
"We've put ourselves in a really good position to do the best job we can do. We need to work together as a team. We'll make sure we do absolutely everything to get the job done."
Qualifying started after a light rain shower and with overcast skies, but the track was drying through the session without a feared downpour.
Germany's Nico Hulkenberg, who was on pole at Interlagos in 2010 for Williams in weather-affected conditions, qualified seventh in his last race for Force India before moving to Sauber.
Finland's 2007 champion Kimi Raikkonen put his Lotus in ninth place with Germany's Nico Rosberg rounding out the top 10 for Mercedes.
Raikkonen's team mate Romain Grosjean was the big loser from qualifying after tangling with the HRT of Spaniard Pedro De la Rosa in the first phase and ending up 18th.
"I was behind Pedro for the whole lap, he had blue flags. I went to overtake him and I don't think he saw me, I braked as much as I could but we made contact," said Grosjean. "In those colder conditions it was difficult to get the tyres up to temperature for the final lap."
Seven times world champion Michael Schumacher will start his last Formula One race in 14th place for Mercedes, ending a three-year comeback at the age of 43.
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