Pawar and Patel sent in their resignations to Prime Minister Manmohan Singh late in the evening. The prime minister is understood to have said he will not accept it, sources told IANS.
The two ministers will not be attending office from Friday, but the party will continue in the alliance, the source added.
The Nationalist Congress Party, with which the Congress shares government in Maharashtra, is upset over the way in which the Congress has "denigrated and humiliated the coalition", party spokesperson D.P. Tripathi told IANS.
The signs of trouble were apparent when Pawar and Patel boycotted the cabinet meeting Thursday evening chaired by the prime minister.
The unhappiness of the ally was rumoured to be over Agriculture Minister Pawar not being given the number two slot following the exit of Pranab Mukherjee.
The boycott of the cabinet meeting by the NCP was the first time in eight years, according to Tripathi.
Both Pawar and Heavy Industries Minister Patel attended a meeting with party leaders when the cabinet was on, a party leader source said.
Though Patel downplayed their absence, telling reporters that nothing should be read into their action, Tripathi was more outspoken.
He said the NCP had "problems in how they (Pawar and Patel) were being treated" in the cabinet. The NCP has nine MPs in the Lok Sabha.
He underlined that it was the "first time in the last eight years" that the NCP had acted in this manner.
Asked if the party was upset that Pawar had not been made the number two in the government after Mukherjee quit the government for presidency, Tripathi said Pawar had never asked for any position.
The spokesman said the "problems were much higher" and would be discussed at a party meeting. He did not elaborate.
He said the NCP has "always supported the policies of the government", and denied that Pawar was hankering after being made the de facto number two.
"Mr Pawar has never demanded anything in his long political life", and added that the NCP has always demanded a "political coordination committee".
Mukherjee had always occupied the seat next to the prime minister at cabinet meetings.
After he quit, Pawar occupied the seat during a cabinet meeting. However, at the last meeting, Defence Minister A.K. Antony took the seat, indicating he had been made the de facto number two.