"Congratulations Prithviraj Chavan for proving that men of principle, integrity& English-language education can also win elections!," Tharoor tweeted.
Chavan, contesting assembly elections for the first time from Karad, defeated the seven-time sitting MLA and Congress rebel Vilas Patil-Undalkar by over 14,000 votes.
However, as the one leading the party in the elections, he failed to retain power and the BJP is at the cusp of forming the next government.
Tharoor, a former UN diplomat, who was recently removed as Congress spokesperson.
Leaders like Tharoor, who have not risen from grassroots politics, have faced muted criticism from within the party, with detractors saying that "paratropping" of such leaders have done no good to the party.
Sections in the party have been maintaining that despite an honest image, Chavan has been a "liability" on Congress and his "non-political" attitude had done more damage to the party than benefitting it.
In another tweet, Tharoor noted that Congress is 23 percent up in Maharashtra as compared to Lok Sabha elections and that he was confident that the "upswing" is beginning.
Party general secretary Digvijay Singh in his tweets, said there was "no need for demoralisation" over the results in Maharashtra and Haryana even as he conceded that there is a "greater challenge" now for the Congress.
"We have done it earlier and we would do it again under the leadership of Sonia Gandhi and Rahul Gandhi. No need for demoralisation.
"Greater Challenge for Congress Party now. We have to go back to the people and win back their trust. Disappointed with Maharashtra and Haryana results. But then only thing constant in Democracy is Change," Singh said in his tweets.