The 29-year-old Portugal captain also scored for Manchester United when they won the Champions League in 2008 in Moscow and capped an astonishing season with his 17th Champions League goal of this campaign at the Stadium of Light.
His penalty conversion contrasted with his miss in the final shootout against Chelsea six years ago.
Ronaldo had already broken the European Cup record of 14 goals in a season established by Jose Altafini of AC Milan 51 years ago and by his rival Lionel Messi of Barcelona in 2011-12 and has now set a new benchmark in the competition.
Ronaldo, the FIFA World Player of the Year, has scored 52 goals in 51 Champions League games for Real and, together with his goals at United, has 67 in the European Cup in total.
That ties him in second place with Messi, while both players are four goals behind Raul who tops the all-time list with 71.
Ronaldo, making a rare club appearance in Lisbon, the city where he came to fame as a teenager with Sporting, had nine goal attempts on Saturday, one less than the entire Atletico team.
"Ever since I arrived at the club I always felt ready for this moment. The pressure is making me a better player every day," he told reporters. "The Decima (10th European Cup) is here now and with records broken along the way it's just awesome."
Ronaldo had not played since limping off with muscle fatigue eight minutes into the La Liga game against Valladolid on May 7 and came out wearing strapping on his thigh.
Although he was not as devastating as he can be, he still had a fine match, creating chances for himself and his team mates, and said: "It was worth taking the risk to play (after injury) - and we are the winners."
Ronaldo was enjoying very different emotions at the stadium than he did there a decade ago when Portugal surprisingly lost 1-0 to Greece in the final of Euro 2004.
This time he was celebrating wildly with his team mates as they came back from the dead to beat Atletico with three goals in extra time after Sergio Ramos's equaliser in stoppage time.
Ronald Koeman can also lay claim to scoring in two European Cup finals for two different winning teams, but his goal for PSV Eindhoven in 1988 came in a penalty shootout after a 0-0 draw with Benfica and does not count in official records.
The Dutchman also scored for Barcelona in a 1-0 win over Sampdoria in the 1992 European Cup.