Both sides had chances in the second period, but Madrid held on for a vital three points.
Here, Sports Mole dissects the 90 minutes of action between the two La Liga rivals.
On target: 5
On target: 3
Was the result fair?
In truth, there was hardly anything between the two teams in terms of general play. If anything, Villarreal were the better side, especially in the second 45 minutes. However, Los Blancos were clinical in front of goal and ultimately secured all the points with two goals in the first period.
As expected, Villarreal had possession of the ball for long spells on their own patch, but struggled to create clear chances against a Real Madrid defence that continues to show signs of serious improvement. Both managers can be pleased with what they saw, but the away side's greater quality in the final third eventually made the difference during what was an entertaining affair.
It was a performance that many would have predicted from Villarreal. They were full of energy and dominated possession for long spells, but they did find it difficult to create clear openings. The introduction of Giovani dos Santos in the second period certainly made the Yellow Submarine more of a threat, while Ikechukwu Uche and Luciano Vietto both had chances throughout the 90 minutes.
On another day, they would have secured at least a point from this type of performance, but they were caught by two Madrid goals of the highest order. It has been a strong start to the season, but they have now been beaten by both Barcelona and Real Madrid on their own patch. In truth, the likes of Bruno and Cani struggled to influence the match for long spells this afternoon as the lack of a final pass cost them.
Real Madrid's performance
It was all doom and gloom at the Bernabeu after Real Madrid lost to Atletico Madrid, with that defeat leaving them with just three points from three games. They have since won all three of their league games, however, and this was perhaps their most impressive performance.
It is always difficult at El Madrigal and Los Blancos entered the match having not won in this stadium on their last two visits. They had to spend long periods of the match without the ball, but ultimately it was their quality that shone through.
Modric's opener was of the very highest order, while Ronaldo's strike was also a demonstration of Real Madrid's incredible threat on the counter attack. Overall, however, head coach Carlo Ancelotti will be more pleased with his side's defensive performance, with Dani Carvajal, Raphael Varane, Marcelo and Sergio Ramos all impressing for the visitors.
Sports Mole's man of the match
Raphael Varane: Real Madrid have not exactly been water-tight in defensive areas this season, while Varane has had to spend some time on the sidelines. The Frenchman has kept his place in the XI in recent weeks, however, and made his point with another strong performance this afternoon. The youngster was aerially dominant, but it was his ability in possession of the ball that impressed the most. He just never looked flustered.
Villarreal's summer signing Vietto had a wonderful chance to send his side ahead in the first period after breaking into the Real Madrid box, but he curled his effort high and wide of the crossbar with just Iker Casillas to beat. It was brilliant work from the forward, but his finish was wayward. A goal at that stage might have made it a different match.
Spanish official Alberto Undiano had a fairly confident afternoon at El Madrigal. The referee issued just the one yellow card throughout the 90 minutes, with Ramos in the book in the first period. Real Madrid had a couple of penalty shouts, but Undiano was not interested despite strong claims. In truth, the Spaniard was not seen for long spells, which is always a good sign for a referee.
Villarreal: The Yellow Submarine continue their Europa League campaign at home to Apollon on Thursday, before travelling to Celta Vigo in the league next Sunday.
Real Madrid: Los Blancos return to Champions League action away to Ludogorets on Wednesday, before continuing their La Liga campaign at home to Athletic Bilbao next weekend.