Team-mate Douglas Costa will be sidelined for the Atletico game because of a thigh strain, Juventus indicated.
Victory in Bergamo was the Bianconeri's fifth in a row in all competitions and they are top of Serie A, one point clear of Inter, but the loss of De Ligt on top of Costa's absence would be a blow to head coach Maurizio Sarri.
Centre-back De Ligt has started 10 of 13 domestic league games this season, with Giorgio Chiellini's knee injury thrusting the €75million signing from Ajax into the spotlight.
Sarri will also monitor the fitness of forward Federico Bernardeschi, who was replaced after 26 minutes against Atalanta having suffered a bruised chest.
A statement on the official Juventus website said: "Following diagnostic tests carried out this morning ... it emerged that Matthjis de Ligt suffered a dislocated right shoulder in yesterday's match and has now began the appropriate therapies and recovery.
"Therapy and recovery also for Federico Bernardeschi, who suffered a bruise to the right hemithorax.
"Douglas Costa suffered a low-grade lesion of the semitendinosus muscle of the right thigh and has started rehabilitation treatment."
Juventus said that in winger Costa's case, it would take around 15 days for him to fully recover.