Ganguly, 50, was survived by his wife and a son.
"He died at 2.45 AM because of multi-organ failure and fat embolism in a case polytrauma after he met with a road accident on Tuesday," said a senior official of the Belle Vue Clinic, where he had been admitted.
His condition turned critical yesterday and he had been put under ventilation with full life support as his parameters had been fluctuating massively.
The noted character actor's condition deteriorated so much that doctors had to cancel the second operation which was slated last afternoon.
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West Bengal Chief Minister, Mamata Banerjee also paid a visit to enquire about his condition, on the day he was admitted.
Ganguly started his career as a stage actor and later worked in television and films.
He acted in acclaimed films like 'Gaynar Baksha' by Aparna Sen, 'Laptop' by Kaushik Ganguly, 'Byomkesh Bakshi' by Anjan Dutta, 'Iti Srikanta' by Anjan Das and 'Mahulbanir Sereng' by Sekhar Das.