Leading 2-0 from the first leg in Madrid, Karim Benzema gave Real the lead a minute before half-time yesterday but Tino Costa levelled for the home side on 52 minutes following Fabio Coentrao's dismissal.
Real also saw Angel di Maria dismissed late on.
Madrid were dealt an early blow when goalkeeper Iker Casillas was forced off a quarter of an hour into the contest with an injured finger, but Benzema ensured Valencia had a mountain to climb as he put the visitors ahead on 44 minutes.
Xabi Alonso's threaded pass found the France striker with just Vicente Guaita to beat and he made no mistake with a composed finish into the far corner.
Madrid were reduced to 10 men four minutes after the break as Coentrao collected a second booking and Costa gave Valencia a glimmer of hope, equalising just moments later.
Valencia sought to capitalise on their man advantage in a frenetic final half hour but Real remained resolute despite having Di Maria sent off for lashing out at Joao Pereira. Sevilla also clinched their berth in the last four following a 4-0 rout of Real Zaragoza.
After a goalless first leg, Zaragoza's cause was hampered by a 26th-minute red card to Jose Manuel Fernandez as Alvaro Negredo and Ivan Rakitic struck before the interval.
Fran Gonzalez then received his marching orders as Zaragoza were reduced to nine men on 65 minutes before further strikes from Negredo and Manu del Moral completed the demolition.
Barcelona travel to Malaga for the second leg on Thursday after the reverse fixture at the Camp Nou finished 2-2, while Atletico Madrid head to Real Betis with a two-goal advantage.