Dybala was substituted straight after scoring the winning penalty in the 48th minute, leaving the pitch with what appeared to be a muscle problem. Medical staff put ice on his left thigh.
"I say [Dybala is] bad. Not to say very, very bad. Unfortunately, it is more very bad than [just] bad," Mourinho told DAZN.
The Portuguese coach added that he imagined it would be difficult for Dybala to return before 2023.
"I'm not a doctor and I haven't spoken to one, but from my experience, from what I understood from talking to Paulo, it [will be] difficult," he said.
The World Cup in Qatar starts on Nov. 20, with Dybala viewed by many as a fringe player for Luis Scaloni's Qatar-bound squad.