Fernandes was a leader of anti-merger movement supporting the cause of Goa remaining as an independent state during the historic 1967 Opinion Poll.
He submitted his resignation in response to the demand made by Goa Sports Minister Manohar Ajgaonkar.
The Congress also slammed the ruling Bharatiya Janata Party for hosting an 'ideology' workshop in Goa for its 27 MLAs, even as the city is facing severe water scarcity.
Last week, Sawant had told the state legislative assembly that entry of native Goans would be banned from the onshore and offshore casinos in the state.
Chodankar said that Sawant should have stayed back in Goa to monitor the flood-like situation in the northern villages of Sal and Ibrahimpur.
The petition has demanded the disqualification of the 10 MLAs, arguing that their split from the party and the subsequent merger into the BJP was unconstitutional.
GPCC chief Girish Chodankar announced on Thursday that she was suspended as the secretary of the committee pending inquiry against her for indulging in anti-party activities.
The state Congress unit has also resolved to shut the door on the rebel legislators, including former Leader of Opposition Chandrakant Kavlekar, during a meeting.
Sardesai also announced that the Goa Forward Party was 'withdrawing' its support to the BJP-led government.
Days after 10 Congress MLAs in Goa joined the BJP, CM Sawant reshuffled his cabinet, dropping three members of ally GFP and an Independent legislator as ministers.
The Congress MLAs are likely to join Goa cabinet. Sawant had hinted earlier that he will soon take a decision on reshuffle of his cabinet after meeting with Nadda.
Congress may not be able to legally stall the split as the rebels constitute two-thirds of its strength in the Goa Assembly and would not invite provisions of the anti-defection law.
The Congress, which had emerged as a single-largest party after 2017 Assembly polls in the coastal state, is now reduced to five legislators.
Naik was the President of Goa Pradesh Congress Committee who had resigned from the post recently after party chief Rahul Gandhi appealed for the young minds to take over the reigns.
The Congress Goa in-charge has claimed that if given a chance they can prove their majority in the assembly within seven days.