The Rojiblancos captain sat out training this morning due to a muscle problem, according to Spanish news outlet Marca.
He now faces a race against time to get fit for the visit of the Red Devils to the Wanda Metropolitano.
The Spanish champions side are already without Felipe Monteiro and Yannick Carrasco, who are both suspended, while Mateus Cunha and Daniel Wass are sidelined with injuries.
Thomas Lemar is also doubtful after testing positive for COVID-19 last week.
Head coach Diego Simeone could be forced to make a few changes to his line-up from the weekend.
Atletico Madrid beat Osasuna 3-0 in Pamplona on Saturday in La Liga, courtesy of goals from Joao Felix, Luis Suarez and Angel Correa.
Atletico Madrid face tense encounter against United
Atletico Madrid and Manchester United meet in one of the most open ties of the round, as both sides have struggled this season.
Since clinching the Spanish title, the Rojiblancos have receded dramatically, losing much of the swagger with which they romped to the summit.
Their defense, too, has been in complete shambles, conceding goals at a rate never seen before under Simeone.
United have also gone through the motions and have barely improved since booting Ole Gunnar Solskjaer as their performances are still lacking.
However, their last two results have shown signs of improvement, with both teams winning in their respective leagues.
Atletico overcame Getafe in a 4-3 thriller before brushing Osasuna aside in a 3-0 win, whereas United saw off Brighton 2-0 followed by a thrilling 4-2 defeat of Leeds.
The sides are also not too familiar with each other, having never clashed in the Champions League before.
In fact, their only pair of meetings came way back in 1991 in the European Cup Winners Cup, where Atletico won the home leg 3-1 before seeing out a 1-1 draw at Old Trafford.
Paul Merson has predicted the results for Chelsea vs Tottenham and other GW 2 fixtures! Click here