A case of cheating, forgery and conspiracy has been filed against Mr Tomar, 49, for allegedly faking degrees.
The minister sent his resignation via his lawyer to Chief Minister Arvind Kejriwal late on Tuesday, from the Hauz Khas police station, where he was taken from court. He has now been taken to the All India Medical Institute of Medical Sciences or AIIMS.
He has said in his letter, "Earlier too I had offered to resign, but you didn't accept it. This time I request you to please accept my resignation."
At AIIMS Mr Tomar told reporters, "I didn't want embarrassment for my party and so resigned...you know very well know why this is happening, the Centre is doing it, Modi is doing it."
AAP has said it will approach a higher court. The Arvind Kejriwal government has alleged "political vendetta" by the BJP-led Centre, with whose representative in Delhi, the Lieutenant Governor, it is engaged in a bitter turf battle.
On Tuesday morning, about 30 to 40 policemen took Mr Tomar away when he was addressing people in his West Delhi constituency. AAP has alleged that they took him away on the pretext of getting some documents and then drove him to one and then another police station, where he was held for hours before being taken to court.
The Delhi Police had sought a five-day custody, the court granted it four. The police is expected to take Mr Tomar to universities in Uttar Pradesh and Bihar whose degrees its alleges he faked.
The police said Mr Tomar was arrested following investigations into a complaint filed by the Delhi bar council alleging that the minister's university and law degrees are fake.
The arrest took the AAP government by surprise. "There is an emergency-like situation in Delhi," said Deputy Chief Minister Manish Sisodia, and asked how the minister could be arrested when the matter is being heard in court.
He also questioned the manner in which the minister was arrested. "Is he the mafia, was he running away?" Mr Sisodia asked.
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