The Brazilian burst into space from inside his own half to double Los Blancos' lead, just 90 seconds after Marco Asensio's stunning strike opened the scoring at the Santiago Bernabeu.
Madrid, having failed to score on Sunday against Real Sociedad, encountered similar frustration in the first half and saw an Antonio Rudiger header disallowed juts before half-time.
That did not deter Carlo Ancelotti's side, who responded in style in a second period where Valencia finished with 10 men after Gabriel Paulista's dismissal.
It took just three minutes for Madrid to carve through Valencia's defence, Luka Modric feeding a pass through to Asensio but a fine save from the boot of Giorgi Mamardashvili kept him at bay.
Asensio had another chance after Karim Benzema's deft backheel into his path inside the area but Gabriel was on hand with an outstanding block to deflect the strike safely over the crossbar.
Los Blancos thought they had found their breakthrough on the brink of half-time, Rudiger flicking a header in off the right-hand post, but referee Javier Alberola Rojas chalked the effort off for a foul from Benzema on Yunus Musah as Modric's corner was whipped in.
Six minutes after the restart, the hosts finally broke the deadlock. It was third-time lucky for Asensio, who picked up possession outside the box and unleashed a ferocious left-footed drive that left Mamardashvili stranded.
The lead was doubled just 90 seconds later, Vinicius bursting into space down the left and driving into the area and slotting a comfortable finish beneath the Valencia stopper.
Valencia's problems got worse when Gabriel was given his marching orders for a horrendous hack on compatriot Vinicius, who was fortunate to avoid injury.