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Madrid started at a bright pace and they almost took the lead after five minutes when defender Sergio Ramos rifled into the back of the net, only to have his effort chalked off for handling the ball in the box.
As expected a stunt organised by Manchester United fans saw a plane fly above El Madrigal showcasing a 'Come home Ronaldo' banner, while below on the pitch Ramos was left to make a stunning interception to stop Uche from breaking the deadlock.
The hosts were made to pay in the 32nd minute as Modric showed his class by lashing home an effort into the bottom corner from outside of the box to make it 1-0.
Villarreal could have equalised just before the break, only for Cani to guide his header just wide of the right post with Casillas scrambling to make ground.
The miss was to prove pivotal as Madrid claimed their second of the afternoon just before half time, as Karim Benzema squared for an on-rushing Ronaldo to slide in and make it 2-0.