The breakthrough arrived in the 14th minute of the clash, with Valverde's strike from distance taking a deflection and landing in the bottom corner, as Real Madrid settled some of the early nerves that had been present following their defeat to Lille last time out.
There was almost an instant response from Villarreal, but Nicolas Pepe's effort came off the crossbar.
Los Blancos enjoyed the better of the opening half of action, having 54% of the ball and boasting nine shots to Villarreal's six, but Valverde's effort was all that separated the two sides ahead of an intriguing second 45 minutes of action.
Without the presence of top goalscorer Ayoze Perez due to an injury, Villarreal found it difficult to get going for long stages at Bernabeu, and they conceded a second in the 73rd minute of the contest, with Valverde this time turning provider to set up Vinicius, who found the back of the net with a thumping drive from distance.
It was another Los Blancos display that lacked a spark for long spells, but it was a professional performance from Carlo Ancelotti's side, who simply had to bounce back from their loss to Lille.
The win has moved second-placed Real Madrid level on points (21) with leaders Barcelona in the La Liga table, while Villarreal remain third, having suffered their second league defeat of the campaign.
REAL MADRID VS. VILLARREAL HIGHLIGHTS
Federico Valverde goal vs. Villarreal (14th min, Real Madrid 1-0 Villarreal)
Real Madrid make the breakthrough in the 14th minute of the contest, and it is a brilliant strike from Valverde, with the midfielder's effort from outside the box landing in the bottom corner, with the help of a deflection.
There did not appear to be too much danger when Valverde picked up the ball, but Valverde's effort is deflected into the corner, and Real Madrid have the lead in the early stages of the fixture.
Vinicius Junior goal vs. Villarreal (73rd min, Real Madrid 2-0 Villarreal)
Real Madrid double their advantage in the 73rd minute of the contest, as Valverde breaks into a forward position before finding Vinicius, who smashes the ball into the back of the net from distance.
MAN OF THE MATCH - FEDERICO VALVERDE
Valverde is not the biggest name in the Real Madrid side, but there are few players more important, and the Uruguay international was again in excellent form against Villarreal on Saturday night.
The midfielder made the breakthrough in the 14th minute before turning provider for Vinicius in the second half, and his constant running in the middle proved difficult for Villarreal to contain.
Valverde also completed 77 of his 80 passes during a dominant performance at Bernabeu.
REAL MADRID VS. VILLARREAL MATCH STATS
Possession: Real Madrid 54%-46% Villarreal
Shots: Real Madrid 11-10 Villarreal
Shots on target: Real Madrid 2-1 Villarreal
Corners: Real Madrid 2-5 Villarreal
Fouls: Real Madrid 7-11 Villarreal
BEST STAT
WHAT NEXT?
Real Madrid will be back in action against Celta Vigo on October 19, before switching their attention to the Champions League, welcoming Borussia Dortmund to Bernabeu three days later for a repeat of the 2024 final.
Villarreal, meanwhile, will be aiming to bounce back from the defeat when they welcome Getafe to Estadio de la Ceramica on October 20.