Miserable, wet conditions shrouded Interlagos throughout all three qualifying segments but come the conclusion it was four-time world champion Vettel who again came out on top.
In the unstoppable Red Bull, Vettel finished six tenths of a second quicker than Nico Rosberg (Mercedes), with Ferrari's Fernando Alonso over a second back in third.
Following a wet final practice session, the rain relented prior to the start of qualifying, allowing the track to dry in places.
However, 30 minutes ahead of the first qualifying period light rain again began to fall, resulting in a queue of cars in the pit lane as the clock counted down towards the start.
Hamilton was the first to cross the line with a lap of one minute 25.342secs, a time that was unable to be bettered as the conditions steadily worsened.
Nine minutes into the initial 20-minute run the rain's intensity was such that all 22 cars headed back into the pits knowing they would be unable to improve.
The final few minutes, with the rain ebbing and flowing, saw a number of the backmarkers take to the track.
Lotus' Heikki Kovalainen was the big winner, vaulting himself away from potential danger up to fifth, whilst Toro Rosso's Jean-Eric Vergne clambered out of the bottom six.
That dropped Pastor Maldonado to 17th, the Venezuelan in his last race for Williams ahead of a potential move to Lotus that could be announced as early as Sunday.
Sauber's Esteban Gutierrez will line up 18th, whilst there were no surprises with the bottom four.
Caterham duo Charles Pic and Giedo van der Garde start 19th and 20th, with Pic and Max Chilton on the back row.
Come the start of the 15-minute middle session, fortunes fluctuated as the rain ebbed and flowed and whether there was enough heat in the intermediate tyres.
Kovalainen just missed out on a place in Q3 by 0.015secs to Sauber's Nico Hulkenberg, the Finn starting 10th ahead of Force India's Paul Di Resta.
Williams' Valtteri Bottas lines up 13th ahead of Sergio Perez who spun into a wall on his final attempt, but at a time when the rain was heavier.
A small crumb of comfort for Perez is he starts ahead of team-mate Jenson Button - who lines up 15th in front of Adrian Sutil in his Force India - with the Mexican outqualifying the Briton 10-9 over the year.
Explaining the difficulties in qualifying, and the potential dangers for the race, Button said: "We struggled because there was so much water, and we haven't run when the conditions were this bad.
"We've been trying to save tyres all weekend for qualifying, but we made the wrong call.
"If it's wet like this on Sunday it's a horrible race because you cant see anything. Hopefully it wont be all under the safety car."
It was at that point the rain began to hammer down, forcing the FIA to delay Q3 by 40 minutes given the safety concerns with so much water on the track.
The conditions meant the drag reduction systems on the remaining 10 cars had to be disabled to ease their top speed.
The full Pirelli wet tyres were also used initially, and with banker laps set, the call was made to switch to the inters.
Not for the first time this season Vettel then blitzed his rivals, with Rosberg and Alonso left trailing by some distance, along with the other seven drivers.
For what will be his 215th and final grands prix before switching to Porsche's sportscar programme for next year, Mark Webber will line up fourth in his Red Bull, with Mercedes' Lewis Hamilton fifth.
Lotus' Romain Grosjean starts sixth ahead of Daniel Ricciardo in his Toro Rosso, followed by team-mate Jean-Eric Vergne.
In his final race for Ferrari after eight years with the team, and a move to Williams, Felipe Massa is ninth on the grid, with Sauber's Nico Hulkenberg 10th.