Real were already 3-0 up from the first leg and headed east to the Vicente Calderon with a huge degree of security.
They would have been expecting a rough ride, especially as Atletico are the holders of the trophy having beaten Los Blancos in last year's final, but it did not turn out that way.
The game was up with just seven minutes gone as Ronaldo was felled by Javi Manquillo and got up to blast in the resulting spot-kick.
His goal served to fire up the home fans even more and they nearly had something to cheer when Raul Garcia thumped the post from 25 yards with Iker Casillas beaten.
But there was a deathly silence with 16 minutes gone as Gareth Bale traded passes with Isco, beat Emiliano Insua for pace and was chopped down. Ronaldo again did the business from 12 yards.
The Portuguese's reward was to be bit by an object thrown from the crowd as he left the field at half-time, but he was able to do so at full-time as a winner.
Both sides had the odd effort in the second half - Ronaldo stabbed into a crowd of bodies and Mario Suarez headed wide when well set - but the damage had long been done.
Barcelona or Real Sociedad will meat Carlo Ancelotti's men in the final.