Kroos’ corner was punched in by Valencia keeper Jaume Domenech as he disorganised back towards his line once remonstrating along with his defenders.
Isco’s volleyed end doubled Real’s lead before Luka Modric created it 3-0.
Daniel Parejo scored a late consolation from the penalty spot once the referee consulted the pitchside var monitor.
The penalty was given for handball by Sergio Ramos despite it showing to be accidental.
Barcelona will face Atletico Madrid within the different semi-final on weekday, with Real facing the winner within the final on Sunday
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