Parsekar, who was unanimously elected the leader at a meeting of the BJP Legislature Party, will succeed Manohar Parrikar after he resigned earlier in the day and is set to join the Union Cabinet.
His name was proposed by Parrikar and seconded by the Deputy Chief Minister D'Souza, who had earlier staked claim to the post on ground of seniority.
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However, he backed Parsekar after being mollified by the party leadership.
"Parsekar was elected the leader of the BJP Legislature Party unanimously," said party general secretary Rajiv Pratap Rudy, party's observer for the election.
Parsekar, MLA from Mandrem constituency, would be sworn-in as Chief Minister at 4 PM at Raj Bhavan today.
Earlier, Parrikar faxed his resignation to Governor Mridula Sinha at Raj Bhavan. The 58-year-old technocrat- turned politician had taken over as Chief Minister in March 2012 after BJP rode to power in the coastal state.