The left back arrived at Stamford Bridge one year ago from Atletico for £15.8m and is returning to the Spanish capital for around £800,000 less.
Luis made 26 appearances for Chelsea and scored his only goal for the club in a 3-1 League Cup victory at Derby in December.
The 29-year-old spent four years with Atletico in his first spell at the club, where he won a La Liga title in 2013/14.
His last match for the club was the Champions League final in the same season, which was won 4-1 by Real Madrid after extra-time in Lisbon.
Luis also played for Deportivo La Caruna for four years before making his move to the Vicente Calderon Stadium in 2010.
The Brazil international won his 18th cap at the recent Copa America in Chile, where Luis played in all his country’s matches before they lost in the quarter-final.