However, a stunner from right-back Mario Gaspar cut the deficit to 2-1 moments before the half-time interval.
Benzema scored Madrid's fourth less than 10 minutes later, however, to make sure of all three points.
The result temporarily moved Madrid into second, but they finished the evening on top after rivals Atletico Madrid lost 2-0 at Almeria in the late kickoff.
Here, Sports Mole dissects the 90 minutes of action between the two La Liga rivals.
On target: 6
On target: 3
Was the result fair?
Villarreal will feel that they could have taken something from their trip to the Bernabeu, but in truth, Madrid did just about enough to claim all the points. The away side found themselves 2-0 behind after 25 minutes despite arguably starting the stronger and it was an uphill task from that moment forward. Both managers can be relatively pleased with what they saw this evening in the Spanish capital, aside from a couple of poor defensive moments for Villarreal.
Without a certain Cristiano Ronaldo, Los Blancos showed that they can find the back of the net with ease. There were a couple of defensive problems this evening, but both of Villarreal's efforts were absolute belters. Angel di Maria and Luka Modric were both terrific for the home side, while Jese found himself among the goals once more as his sensational campaign continues. It appears that Carlo Ancelotti's side are starting to hit top form at the perfect time of the season.
The Yellow Submarine might have lost this evening, but it is difficult to be too critical of the newly-promoted outfit, aside from a couple of defensive errors. It would have been easy to collapse when they fell 2-0 behind and indeed 3-1 in the second half, but they responded on both occasions. In the end, they were unable to recover for a third time, but they can take plenty of positives from the match. Had the likes of Cani and Ikechukwu Uche been fit and available, then it might have been a different story.
Sports Mole's man of the match
Karim Benzema: The French forward continued his impressive run of form this evening with a brace. The 26-year-old's first goal was a smart finish at the near post, while his second was a brilliantly placed effort into the bottom corner. The former Lyon striker has now scored 17 times this season, just three short of his total in the previous campaign.
Villarreal defender Jose Dorado had a horror show in the early stages when he took too long to clear the danger on the edge of his own box. The centre-back's lack of concentration allowed Bale to nip in and send the home side into the lead. Dorado was also guilty of pushing Benzema to the ground inside the box in the second period, but the referee did not spot the incident. It perhaps should have been a penalty.
In truth, Jose Gonzalez had a relatively simple evening in the Spanish capital. There were a number of feisty challenges throughout the 90 minutes, but the Spaniard was always on hand to calm proceedings. Madrid will feel that they should have had a penalty in the second half when Dorado pushed Benzema to the ground, but aside from that, neither manager will have had too many complaints about his performance.
Madrid: Los Blancos are in Copa del Rey semi-final action against Atletico Madrid on Tuesday. Ancelotti's side hold a 3-0 lead from the first leg at the Bernabeu.
Villarreal: The Yellow Submarine will attempt to return to winning ways in La Liga when they welcome Celta Vigo in the late start next Saturday evening.