After passing up a host of chances in the first-half, Madrid finally made the breakthrough when Karim Benzema tapped home from close range 11 minutes into the second period.
Cristiano Ronaldo then sealed the three points when he bulleted home a header from Isco's pin-point cross 21 minutes from time yesterday.
Barca's shock 1-0 defeat to Malaga on Saturday means the Catalans have it all to do in the final 14 games of the season with the two sides set to meet at the Camp Nou on March 22.
"It is clear we have the advantage at the moment, but as I have said many times this league will be decided in the final game."
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Madrid started brightly at the Martinez Valero and should have been well in front by half-time.
Gareth Bale had an early strike ruled out for offside before Ronaldo smashed an effort from 20 yards off the post.
The World Player of the Year then passed up a huge chance when he miscued with the goal gaping from Bale's low cross.
And the visitors were unfortunate not to be ahead in stunning fashion when Benzema's overhead kick was also chopped off for the tightest of offside calls.
Madrid captain Iker Casillas was making his 500th La Liga appearance, but had barely touched the ball until he had to make a smart low save to his right to deny Aaron Niguez two minutes after the break.
Niguez was lucky to stay on the pitch moments later when he only saw a yellow card for a horrific challenge on Bale that fortunately the Welshman was able to shake off.