The England international invoked memories of the pair's triumph over Chelsea in Moscow in 2008 ahead of Saturday's match, which Real Madrid went on to win 4-1
Before the match, Rooney tweeted his former Manchester United team-mate and invoked the memory of the pair's triumph over Chelsea in the competition in 2008, saying: "All the best tonight Ronnie remember Moscow."
Ronaldo went on to score Madrid's fourth goal from the penalty spot in extra time as Los Blancos secured their 10th European crown over their city rivals at Estadio da Luz.
In doing so, the reigning Ballon d'Or winner broke the record for goals in a single Champions League season (17) and became the first player ever to score in two finals for different winning teams.
Ronaldo and Rooney have not always been on such good terms. In the aftermath of the 2006 World Cup, relations between the two men briefly soured as a result of Ronaldo's perceived role in getting his United team-mate sent off by referee Horacio Elizondo during Portugal's quarter-final clash with England.
Thanks for the support @WayneRooney. Crazy days these last ones!— Cristiano Ronaldo (@Cristiano) May 27, 2014
But the incident was quickly forgotten and the two men went on to win three consecutive Premier League titles together at Old Trafford, as well as the 2008 Champions League final after victory over Chelsea on penalties in Moscow - with Ronaldo heading the opening goal of the match before missing in the shootout.
Ronaldo and Rooney could meet again if England encounter Portugal in the knockout stages of this summer's World Cup in Brazil.
See all Ronaldo's 17 Champions League goals: