And for the second time this season having already scored the winner to hand Real the Copa del Rey against Barcelona last month, Bale scored the crucial goal when he headed into an empty net after Thibaut Courtois had parried Angel di Maria's effort.
With Atletico committed to finding an equaliser, Real were able to counter-attack at will and Marcelo killed the game off when his low shot had too much power for Courtois before Ronaldo sealed his return to Lisbon with a fourth from the penalty spot.
Atletico's top scorer Diego Costa had been surprisingly included in Diego Simeone's starting line-up despite suffering a hamstring injury just seven days ago as Atletico clinched the La Liga title against Barcelona.
However, the Brazilian-born striker lasted just nine minutes as he hobbled off to be replaced by Adrian Lopez.
After a quiet start the game came to life just before the half hour when Raul Garcia was shown a yellow card for chopping down Di Maria and Ramos joined him in the book for squaring up to Garcia.
Ronaldo's resulting free-kick was comfortably dealt with by Courtois, but Real missed a golden chance to open the scoring minutes later through Bale.
The Welshman pounced on Tiago's errant pass in midfield and scampered forward into the area but side-footed wide on his favoured left foot.
Three minutes later it was Atletico who took the lead as Juanfran headed a cleared corner back into the box and Godin took advantage of indecision by Iker Casillas to loop the ball over the Spanish captain and just over the line.
Ronaldo had a couple of half-chances to level at the start of the second-half as Courtois awkwardly tipped another free-kick from distance over before the Portuguese captain headed just wide from a corner.
Taking risks:
As Real took more risks to find the equaliser, though, Atletico were also becoming more dangerous on the break and Adrian was unfortunate to see his goalbound effort deflected just wide by Sami Khedira.
Bale wasted another good opening as he sprinted onto Ronaldo's pass, but chose the wrong option in trying to squeeze the ball home at the near post and dumped the ball into the side netting.
Just when Atletico thought they had the trophy won, though, Real got their reward as Ramos rose to power Luka Modric's corner past the helpless Courtois.
Atletico's tiredness then showed in the second period of extra time as Real had too much pace and power and finally went in front 10 minutes from the end when Di Maria burst into the area and despite his effort being saved by Courtois, Bale was on hand to head in at the back post.
Courtois also got a hand to Marcelo's low drive eight minutes later, but the Belgian international couldn't keep it out.
And Ronaldo got the goal he craved back in his homeland when he was clipped by Gabi moments later and got back up to slam the resulting penalty home.
