Diego Simeone's side had won three of their four games since football's return ahead of hosting Alaves, and there were to be no slips at home as they further tightened their grip on third place.
Saul Niguez got the game's opener just shy of the hour mark, as it was looking like Los Rojiblancos might never make the breakthrough.
That lead was doubled within 15 minutes though as Marcos Llorente was fouled inside the box after a superb run down the right, leading to a penalty which Diego Costa converted to effectively seal the points.
Alaves caused some nerves late on when Joselu scored his own penalty, but Simeone's men were able to see things out for the three points.
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