Skomina was the referee in the 3-2 win Los Blancos achieved against City back in 2012, a score that would be good enough for Madrid to advance to the Final this time.
Back then, Edin Dzeko and Aleksandar Kolarov built a 2-0 lead for City but Madrid ended up clawing their way back with goals from Marcelo, Karim Benzema and Cristiano Ronaldo.
Skomina was born in Koper in 1967 and has been refereeing international matches since 2003.
The Slovenian referee has not officiated a Real Madrid match this season but the record for Los Blancos with him in charge is positive, with four wins and two losses.
Skomina will be helped by his countrymen Jure Praprotnik, Robert Vukan, Matej Jug and Slavko Vincic.