Real went ahead early on through a Cristiano Ronaldo free kick, before the Portuguese set up Mesut Ozil for the second in the second half.
Atletico were unable to muster any real resistance but remain five points ahead of Real in second.
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Since Guus Hiddink arrived at the helm, Chelsea have improved considerably after a tricky start to the campaign.
Newcastle United are staring down the barrel of relegation to the Championship for the second time in the past eight years.