68-year-old Chavan drove to Raj Bhavan this evening and submitted the resignation of his government to Governor C Vidyasagar Rao, official sources said.
It was not immediately known if he has been asked to continue in a caretaker capacity or the state will be brought under a brief spell of President's rule before the Assembly elections next month.
Chavan had called on the Governor earlier in the day too and apprised him of the political developments.
NCP's insistence on the two allies contesting an equal number of the state's 288 Assembly seats and the demand for rotational chief minister were the sticking points during the seat-sharing talks which eventually led to the collapse of the alliance.
Meanwhile, the Raj Bhavan sources said, "The governor is seeking legal opinion (on the future course of action)."
Last night, soon after announcing the breaking up of NCP's alliance with the Congress, NCP leader Ajit Pawar met the governor and informed him that the NCP had withdrawn its support to the government.
He was brought in as Maharashtra Chief Minister in November 2010 after the Adarsh housing scam led to resignation of his predecessor Ashok Chavan.
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