The third 2011 one-two was a fitting finale for Red Bull but Vettel clearly wanted to complete his total dominance with a 12th season victory and had to be told by his team to look after his car.
Webber got his seventh career win in 1 hour 32 minutes 17.464 seconds for the 71-lap race at Interlagos from Vettel, Jenson Button of McLaren and Ferrari's Fernando Alonso, while Lewis Hamilton's modest season ended in the 48th lap with a gearbox failure.
Having wrapped up back-to-back titles last month at Suzuka, Vettel topped the final standings with 392 points from 19 races with 11 victories and six further trips to the podium which he only missed in Germany in fourth place and a first-lap retirement in Abu Dhabi.
The 2009 champion Button was second on 270, Webber third on 258, two-times ex-champ Alonso fourth on 257 and 2008 winner Hamilton on 227.
Vettel is the youngest double world champion, got a season record 15th pole on Saturday and is also the man with the most leading laps in an F1 season which was shortened by one race after the season-opener in Bahrain was cancelled because of political unrest.
Red Bull won a second straight constructors' title ahead of McLaren and Ferrari.
Vettel comfortably won the start from Webber while Alonso shot past Hamilton into fourth and then also got past the second McLaren of Button in the 11th lap.
The 2009 champion Button started the first swing of pit stops five laps later, shortly after Vettel was told by his team that he had a gearbox problem.
Bruno Senna was harshly handed a drive-through penalty for slicing up the right rear tyre of Michael Schumacher with his front wing in a fight for positions in midfield - the puncture sending the record champ Schumacher to last place as he had to limp to the pits to get a fresh rubber, finally placing 15th.
There was more bad news for the German camp when Red Bull informed Vettel that his problem was "serious" and soon after let Webber pass for the lead in the 30th lap.
To add to the spice, Hamilton then also encountered gearbox problems and it failed for good in the 48th lap, a somewhat fitting end a mediocre season by his standard.
Up front, Vettel stayed close behind Webber before being slammed by Red Bull for posting a fastest lap instead of looking after his car.
Button passed Alonso for third with nine laps left but Vettel was too far away for further improvement even though the German rode off the track briefly in the closing stages.