However, Croatia international Sime Vrsaljko has returned to Diego Simeone's 21-man squad for the crucial Champions League clash after missing recent games due to a problem in his back.
Augusto Fernandez will also make the trip to London even though the Argentine midfielder didn't train with the rest of his available teammates on Monday morning.
Juanfran has been out of action since suffering a hamstring injury in his left leg in the preparation for the Champions League clash with AS Roma on 22 November, when Los Colchoneros secured a 2-0 victory to keep their hopes of qualifying for the knockout stages of the competition alive.
The Spaniard missed the subsequent three wins over Levante, Elche and Real Sociedad and will remain on the sidelines for the key clash with Chelsea.
Juanfran's absence is an important blow for Simeone as the 32-year-old right-back would surely have make the starting line-up at Stamford Bridge if he had been fit.
Simeone has recovered his other specialist for that position with Vrsaljko returning to the squad.
However, the Croatian has not played a game since October and it is still uncertain whether he will make the line-up to face Chelsea amid reports linking him with a January move away from the club.
Versatile midfielder Thomas Partey has impressed in that role in recent games while centre-back Jose Maria Gimenez has also covered the position in the past when Simeone has opted for a more defensive alternative.
Meanwhile, the Atletico boss will have less doubts over who to select in attack with Antoine Griezmann being back to his best in recent games.
The France international has scored four goals in his last three appearances, including one during the weekend 2-1 victory over Real Sociedad as Atletico came from behind to move within six points of leaders Barcelona in the La Liga table.
Griezmann's goals wills surely be needed on Tuesday night with Atletico needing to beat Chelsea and hope Roma fail to do so at home to Qarabağ FK to book a place in the last 16 as group runners up.
Atletico lost 2-1 to Chelsea at the New Wanda Metropolitano and will visit Stamford Bridge with only six points from five group games, leaving them two points behind Roma and four adrift of the Blues in the Group C.
Chelsea, meanwhile, have already qualified for the next round but Antonio Conte is still expected to deploy as strong line-up with the Blues needing a victory to progress as group leaders.