Ali, who teaches Urdu at the NDA, was produced before a special court, which remanded him to police custody till May 26.
Ali was arrested on Sunday night. He is the ninth accused arrested in the Mulund blast case.
Twelve persons were killed when a bomb planted in a ladies' first-class compartment of a Mumbai
local went off just seconds after the train entered Mulund station.
A senior police officer said Ali had links with the banned Students Islamic Movement of India and Lashkar-e-Tayiba.
Ali had allegedly provided shelter to three Lashkar-e-Tayiba militants in his Pune house.
Police also believe that a major part of planning for the Mulund blast was done at Ali's place.