From the Sena, party President Uddhav Thackeray's trusted lieutenants, legislature party leader Eknath Shinde and Subhash Desai were present.
The Congress was represented by former Chief Ministers Sushilkumar Shinde and Prithviraj Chavan, former state president Manikrao Thakre and former Leader of Opposition Vijay Wadettiwar.
The NCP had deployed its state chief Jayant Patil, Mumbai President Nawab Malik and former Deputy Chief Minister Chhagan Bhujbal.
The sources said that these meetings were preceded by a short meeting held between Thackeray and Congress-NCP leaders, details of which are not clear.
Thursday's meetings were held in "a very cordial, free and frank atmosphere" and the discussions chiefly pertained to the Common Minimum Programme (CMP) being worked out by the three prospective allies.
Talks also veered around crucial issues of government formation, the post of Chief Minister and Deputy Chief Minister, the sharing of ministries, etc, and all the details are expected to be finalised very soon after the respective parties' green signal to the CMP.
Congress MP Hussain Dalwai said that "the talks are progressing very positively on all sides" but declined to elaborate.
Addressing the media after emerging from one round of the meetings, Wadettiwar said that there was a threadbare discussion on the CMP draft with near-unanimity on most points achieved after comparing the manifestos of the three parties.
"Later tonight, this draft will be submitted to the high command of the Congress, NCP and Shiv Sena for their approval, before it will be finalised. The challenge before us is not to form the government, but to sustain it for a full term, that's why we are discussing all issues very minutely," he said.
Though clarity has not emerged on the post of Chief Minister, the Congress has indicated it is not a claimant for the post, but instead would settle for the Speaker, Deputy Chief Minister and some ministerial posts.
NCP President Sharad Pawar, who is currently on a tour of eastern Maharashtra, is likely to meet Congress Interim President Sonia Gandhi in New Delhi this weekend.
Congress sources also indicate that the final announcement of the proposed three-party alliance is likely to be made by the three parties jointly in New Delhi.
The meetings on Thursday came after a marathon round of independent meetings of the sub-committees of the Congress and the NCP on Wednesday, followed by their joint meeting which ended post-midnight in which they finalized the CMP which was discussed with the senior Sena leaders.
All parties have individually and jointly assured that the new government would be in place at the earliest to bring the state out of President's Rule.
( With inputs from IANS )