"We lost the championship before today, not in Brazil," said Alonso, who agreed with others that it was one of the hardest races he had ever driven.
"It was a lot of risk every lap to crash and have an accident. We could not afford that for sure because we needed a podium finish to have any chance so it was a very delicate situation."
Button, who also won the first race of the season in Australia, took his career tally to 15 wins.
McLaren's Lewis Hamilton had led from pole position but could not shake off his team mate, who made a wise decision to do a long first stint on slicks along with Force India's Nico Hulkenberg.
Hamilton's last race for McLaren before he joins Mercedes ended when he and Hulkenberg collided on the 54th lap as they came up to lap back markers into turn one.
Hulkenberg, who had led for much of the race and skidded into the blameless Hamilton, was able to rejoin but was given a drive through penalty that ended his hopes of a podium finish and seemed harsh given the treacherous conditions.
"I am happy for the team that we got a win and feeling good for the future. I feel numb, a little bit like I did in 2007, it is mixed emotions at the moment," Hamilton said, referring to the title he missed in his first season by a single point when he finished seventh in Brazil.
Image: McLaren Mercedes driver Jenson Button of Britain lifts the trophy after winning the Formula One Brazilian Grand Prix at Interlagos race track in Sao Paulo, Brazil, Sunday, Nov. 25, 2012. Red Bull driver Sebastian Vettel, of Germany, 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 Button under pouring rain.