Spain international Rodrigo Moreno put Marcelino's side ahead in the 19th minute by playing a smart one-two off strike partner Simone Zaza and sliding the ball home from close range.
Italian forward Zaza turned in a free kick from Daniel Parejo to consolidate his side's lead in the 34th, although Ruben Sobrino gave Alaves a foothold in the game by getting a goal back four minutes into the second half.
Hopes of a comeback from the Basque side were short-lived, however, as defender Victor Laguardia diverted a cross into his own net five minutes later.
Valencia are third in the standings after 29 games with 59 points, two above Real who host Girona on Sunday, and 14 clear of fifth-placed Sevilla who go to Leganes.
Marcelino's side will qualify automatically for next season's Champions League by finishing in the top four.
Valencia began the season in fearsome form and were considered title candidates alongside Barcelona until December, when their form tailed off. They are currently on a resurgent run of six wins in their last seven league games and Marcelino praised his side for getting back on track.
"In January we went six games without winning but we have recovered very well and we are flying right now," he told reporters.
"I've been pleased with how we've played throughout the year. When you win many games it looks easy but the coach and players know it isn't.
"I think we're a better team than we were in October. We may not be as electric as then, perhaps we're not as decisive, but we are a better team."
Also on Saturday relegation-fighting Deportivo La Coruna drew 1-1 at home to fellow strugglers Las Palmas, leaving the two sides seven and six points adrift of safety respectively.
Getafe came from behind to win 2-1 at Real Sociedad, prompting an angry reaction from supporters at a soaking wet Anoeta stadium and piling more pressure on beleaguered coach Eusebio Sacristan, whose side sit 14th in the standings and have lost four of their last six games in all competitions.
Leaders Barcelona host Athletic Bilbao on Sunday and second-placed Atletico Madrid play at Villarreal.
(Reporting by Richard Martin, editing by Ed Osmond, Neville Dalton)
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