Directed by Suparn Verma, "Aatma", which released Friday, also stars Bipasha Basu.
Nawazuddin received the special mention for four of his films - "Kahaani", "Gangs of Wasseypur", "Dekh Indian Circus" and "Talaash".
"You should work according to your instinct. It is definitely the most prestigious award and that means appreciation for your work, " he added.