Vettel ended the season with 281 points to 278 for Alonso, who would have been the youngest triple champion at 31 had results fallen his way. Kimi Raikkonen was third overall for Lotus on 207 in his comeback year.
Red Bull had already won the constructors' title for the third year in a row.
"It's very difficult to find the right words, especially after the race today," said Vettel. "I think everything that could go wrong, went wrong.
"To limp home, underneath the safety car (conditions), I didn't know if it was enough...we had to really fight until the end."
On a day when the Brazilian weather produced a thriller to stand the test of time against some of the sport's great races, it seemed the gods were on Alonso's side almost as soon as the starting lights went out.
Image: Mercedes Grand Prix driver Michael Schumacher of Germany, right, greets Red Bull driver Sebastian Vettel of Germany after the Formula One Brazilian Grand Prix at the Interlagos race track in Sao Paulo, Brazil, Sunday, Nov. 25, 2012. Vettel overcame a first-lap crash to clinch his third straight Formula One championship title on Sunday, finishing sixth in an incident-filled Brazilian Grand Prix won by Jenson Button under pouring rain.