Madrid stay third in the Primera Division table on 78 points, one behind leaders Barcelona and second-placed Atletico.
Madrid were missing Gareth Bale and Dani Carvajal through injury but looked the stronger team against fourth-placed Villarreal, although they took their time to break down Marcelino’s side.
Benzema had an early shot saved by Asenjo, who also denied Ronaldo, and defender Eric Bailly made a vital block to prevent Toni Kroos from playing in Benzema in the box.
The Frenchman finally put Madrid in charge after 41 minutes, arriving at the near post to head into the net as Asenjo failed to hold Ronaldo’s cross from the left.
Madrid could have lost their lead just before the break though and needed Keylor Navas to tip away a shot from Denis Suarez, who could have crossed to Cedric Bakambu at the far post.
Modric came close to doubling Madrid’s advantage early in the second half but his shot was deflected just wide of the near post.
Instead it was Vazquez who got the crucial second goal, playing a one-two with Benzema down the right and sending the ball crashing past Asenjo at the near post.
Modric then got the goal he craved, sliding in to meet a cross from Danilo on the volley.
But Madrid’s celebrations were dampened by the image of Ronaldo walking off the pitch before the final whistle, clutching the back of his thigh.
Zinedine Zidane had already made the maximum three substitutions, and Ronaldo was unable to remain on the pitch for the final minutes of injury time.
Victory came at a cost though and Cristiano Ronaldo was unable to finish the game due to a suspected muscle injury.
The Portuguese walked off the Bernabeu pitch in injury time clutching the back of his thigh and his place in the team for next week’s Champions League semi-final first leg with Manchester City could be in doubt.
Fernando Torres’s sensational form kept Atletico in the race as he scored for the fifth consecutive game with a towering header from Antoine Griezmann’s cross for the only goal of the game seven minutes before half-time in Bilbao.
However, victory came at a cost for Atletico as inspirational defender Diego Godin limped off with a hamstring injury that is likely to see him miss at least the first-leg of their Champions League semi-final against Bayern Munich.
Even without Godin, Atletico handled Bilbao’s aerial bombardment to register their 31st clean sheet of the season and keep their title hopes very much alive with three of their last four games to come at home.
