Ronaldo was stretchered off in the first half after being injured by Dimitri Payet, but returned to the touchline to see Eder's long range strike settle the game at Stade de France.
"It was not the final I wanted, but I am very happy," Ronaldo said.
"It is a trophy for all the Portuguese, for all immigrants, all the people who believed in us, so I am very happy and very proud."
Portugal centre-back Pepe, voted the man of the match, said: "We said we would win it for him and we managed to do that."
Twelve years after losing 1-0 to Greece as hosts of Euro 2004, Portugal inflicted the same fate on France, who were seeking a cathartic victory eight months on from the Paris attacks that left 130 people dead.
France coach Didier Deschamps had hoped to lead his country to a fourth major tournament win, and third on home soil after Euro 1984 and the 1998 World Cup, when he was captain.
But it was Portugal skipper Ronaldo who hobbled up the steps to lift the trophy beneath a shower of silver tickertape.
"The disappointment is there and it's immense," Deschamps told French television.
"We've let a big chance to be champions pass us by. There are no words to describe this feeling."
- 'Ugly duckling' -
"Football is cruel, but it's also magnificent. It allows us to experience wonderful times and sad times too," said France striker Antoine Griezmann, whose six goals earned him the Golden Boot award.
The result ended Portugal's run of 10 straight defeats against France, who had eliminated them in the semi-finals at Euro 1984, Euro 2000 and the 2006 World Cup.
They took the spoils in France despite having won only one match inside 90 minutes -- the 2-0 semi-final victory against Wales -- in the whole tournament.
Coach Fernando Santos, who dubbed his team "the ugly duckling", said: "We have a bright future, but right now we need to celebrate."
Victory was especially sweet for Real Madrid superstar Ronaldo, despite his early exit.
He had shed tears as a 19-year-old after Greece's Euro 2004 win in Lisbon, wept as he was carried off on Sunday and cried again as he raced on in celebration at full-time.
In winning a major tournament he surpasses Portugal greats Eusebio and Luis Figo.
Having also won last season's Champions League, he has a stolen a march on his great rival Lionel Messi, who announced his Argentina retirement two weeks ago, in the race for the next FIFA Ballon d'Or.
Taken off in the 25th minute, he returned at the start of extra time to deliver on-pitch pep talks that appeared to inspire his team to victory.
Eder saw a header pushed out by France goalkeeper Hugo Lloris, while Raphael Guerreiro hit the bar from a free-kick.
With 11 minutes of the extra period to play, the killer goal arrived as Eder held off Laurent Koscielny and drove a crisp shot into the bottom-left corner from 25 yards.
"Cristiano told me I would be scoring the winning goal," Eder said. "He gave me strength and positive energy."
- Ronaldo applauded -
The sultry night began with a swarm of moths flitting around the French national stadium and littering the playing surface.
There was an early exchange of chances -- Nani shooting over for Portugal, Griezmann's header drawing a fine finger-tip save from Rui Patricio -- before Ronaldo took centre-stage.
A juddering knee-on-knee challenge by Payet in the eighth minute left Ronaldo writhing on the turf and after attempting to play on, he dropped to the ground, tears filling his eyes.
After having his left knee heavily strapped, Ronaldo re-entered the fray, only to go down again, flinging his armband to the floor.
A stretcher was brought on and as the Portugal captain was carried off, to be replaced by Ricardo Quaresma, the whole stadium rose to applaud.
France's Moussa Sissoko stepped into the spotlight vacated by Ronaldo, driving a left-foot shot over the bar and then stinging Rui Patricio's palms after nutmegging Adrien Silva with a slick Cruyff turn.
But it took the 58th-minute introduction of Kingsley Coman to enliven France. The Bayern Munich winger crossed for Griezmann to head over and released Olivier Giroud for a shot that Rui Patricio parried.
Rui Patricio also repelled a 25-yard effort from Sissoko and when France substitute Andre-Pierre Gignac neatly sidestepped the fit-again Pepe in stoppage time, he could only scuff his shot against the post.