Coach Unai Emery has managed to hang on to the gifted Spain trio despite the club's financial woes and Valencia are increasingly looking like potential challengers to the dominance of Barcelona and Real Madrid with two fine wins out of two.
The three clubs are locked together at the top of the standings on six points.
Silva made up for his lack of height with a perfectly timed run to nod in Mata's cross on 10 minutes before Nauzet levelled when he rammed in a loose ball after Miguel Angel Moya had parried Fabian Canobbio's shot.
Villa, who also struck the bar, put Valencia back in front just after the half hour, turning in a Pablo Hernandez centre, and Mata raced clear to slot through the legs of Valladolid goalkeeper Jacobo Sanz just before the break.
Miguel Monteira sent Villa through on goal 10 minutes after the restart to finish low past Sanz and giant Angola striker Manucho pulled a goal back in the 66th minute.
Earlier on Sunday, Borja Valero's free kick evaded a crowd of players and beat goalkeeper Diego Lopez to earn Real Mallorca a 1-1 draw at rain-soaked Villarreal.
In other matches, Deportivo La Coruna beat visiting Malaga 1-0, promoted Tenerife bagged a 2-1 home win over nine-man Osasuna and Almeria lost 1-0 at Sporting Gijon.
TWO FROM TWO
Champions Barcelona and Real both made it two La Liga wins out of two on Saturday.
Sweden striker Zlatan Ibrahimovic scored one and set up Lionel Messi for a rare header in Barca's 2-0 win at Getafe.
Portugal winger Cristiano Ronaldo came off the bench to seal Real's 3-0 victory at Espanyol with a typical run and finish in added time after Brazilian playmaker Kaka had set up Esteban Granero and Guti.
Sevilla thumped Real Zaragoza 4-1 and Atletico Madrid were held 1-1 at home by 10-man Racing Santander.
Sunday's torrential downpour at Villarreal's Madrigal stadium left large puddles of water on the pitch and the players struggled to control the ball in the second half.
Striker Giuseppe Rossi was in the right place when the ball ricocheted off Israeli goalkeeper Dudu Aouate in the 54th minute and his close-range shot went through the legs of defender Jose Carlos Nunes into the net.
Lopez was unable to keep out Valero's low strike with a quarter of an hour left and Villarreal were held to a second draw in their two La Liga matches this season after a 1-1 scoreline at Osasuna.
"We are happier than after the Osasuna match because the team played better, especially in the first half, even if in the second it was much harder because of the downpour," Villarreal coach Ernesto Valverde told a news conference.
Promoted Xerez's first ever top-flight match at home ended in defeat when they lost 1-0 to Athletic Bilbao and had a player sent off near the end of Sunday's late game.
