Barcelona improved in the second period, but Ronaldo struck once more to move Madrid into a 3-1 lead on aggregate.
It was 3-0 on the evening after 68 minutes, however, when Raphael Varane thumped a header into the back of the net.
Jordi Alba handed Barcelona a late consolation, but it was a case of too little too late as the Catalan outfit exited the competition.
Read how it all unfolded in Sports Mole's minute-by-minute live commentary of the action below.
BARCELONA: Pinto, Alves, Pique, Puyol, Alba; Busquets, Xavi, Fabregas; Pedro, Messi, Iniesta
REAL MADRID: Lopez; Arbeloa, Ramos, Varane, Coentrao; Alonso, Khedira; Ronaldo, Ozil, Di Maria; Higuain