Carlo Ancelotti’s side looked as if they were still feeling the effects of the late loss in Paris and almost found themselves behind midway through the first half.
Casemiro’s error left Alavés winger Jason with a free shot from 15 yards but the Spaniard jumped his shot.
At first, it sounded like it was going to be another frustrating night for Los Blancos but Marco Asensio broke the deadlock in the 63rd minute to allay the home side’s concerns.
The 26-year-old cuts in with his left foot and bends the shot into the top corner past dangerous Fernando Pacheco.
Karim Benzema then hit the post before Vinícius Junior doubled his profit with 10 minutes left, hitting the back of the net after a brilliant game between Benzema and Asensio.
Benzema then scored his first goal since returning from injury, withdrew from penalties during the suspension.
Real extend their lead to LaLiga back to seven points when Sevilla faces Espanyol on Sunday.