Michael Schumacher, seven-time world champion, finished fourth in the final Formula One race of his career after a ninth-lap puncture forced him back in the field ruling out any chance of victory, while Briton Jenson Button was third for Honda.
Massa drove to his second career win with ease, finishing 18.6 seconds ahead of Alonso, making him the first Brazilian to win at the Interlagos circuit since the great Ayrton Senna in 1993.
"It was amazing to see Senna winning the Brazilian Grand Prix and the people running on the track. I saw the same today and it was very nice," said a proud and jubilant Massa.
"It's just a dream come true. I always dreamed to have this day in my life and I got it.
"I had such an incredible car, I could control the pace from beginning to end," the Sao Paulo born driver added.
"I never expected to be here in this place today."
World champion Alonso drove a controlled race knowing he just had to finish in the points to secure his second successive title, and with Schumacher the only threat back in the pack due to his puncture, the title was comfortably won.
"Thank you, thank you. Thank you for all these years, it has been a pleasure to work with you," exclaimed Alonso over his car's radio after crossing the line to become Formula One's youngest double champion.
Back-to-back world champion
Fernando Alonso in Brazil
"It's been a fantastic weekend and I need some time to believe I am champion again.
"It's my last race for Renault and a fantastic way to finish the relationship," added Alonso who will drive for the McLaren team next year.
"I will have these memories all my life."
Renault also scored back-to-back constructors' titles, thanks to Alonso's win and teammate Giancarlo Fisichella's sixth, with 206 points to Ferrari's 201.
Bowing out with pride
For Schumacher, even though he did not get on the podium in his last race, his legacy will not be forgotten with a stirring performance after an early set-back.
Starting from 10th on the grid, the German driver quickly made his way up to sixth, but just after overtaking Fisichella for fifth, the Renault driver appeared to clip Schumacher's rear left tyre causing a puncture that would send him back to last place.
Michael Schumacher waves
farewell after his final Grand Prix
Television replays were inconclusive but Ross Brawn, Ferrari technical director, blamed the Italian driver for the puncture.
"I think Giancarlo clipped Michael's tyre as he went past him and screwed our race. So it's very unfortunate because we had by far the quickest car today," Brawn said on Germany's Premiere television.
Schumacher, rejoining the race in 17th place then drove like a man possessed, clocking the fastest lap times and racing through the field back into points contention.
The 37-year-old passed car after car reminding everyone watching of his ability and desire, finally finishing fourth in a memorable performance.