Los Colchoneros have been dealt a blow with the news the defender will be out until March after coming off injured in the defeat to Real Madrid on Tuesday
The 19-year-old was forced from the field in the 44th minute of his side's 2-0 Copa del Rey semi-final defeat to Real Madrid following a collision with Cristiano Ronaldo.
Manquillo landed awkwardly after an aerial battle with the Portugal international, landing on his face and placing considerable pressure on his neck and back.
Atletico released a statement on Wednesday that confirmed a CT scan would rule him out of football for "four to six weeks".
The club also stated that a "fracture of foil of C7 vertebra without displacement" would see him remain in hospital until Thursday.
Manquillo has not been a regular for Atletico this season, making just seven appearances in all competitions.