Banerjee shared the award with his French-American wife Esther Duflo and another American economist Michael Kremer for their 'experimental approach to alleviating global poverty'.
'Congratulations to Abhijit Banerjee on being conferred the 2019 Sveriges Riksbank Prize in Economic Sciences in Memory of Alfred Nobel. He has made notable contributions in the field of poverty alleviation,' Modi wrote on Twitter.
He also congratulate Esther Duflo and Michael Kremer for wining the Nobel.
Born in Mumbai, the 58-year-old economist is currently the Ford Foundation International Professor of Economics at the United States-based Massachusetts Institute of Technology (MIT).
He studied at the University of Calcutta and Delhi's Jawaharlal Nehru University before receiving his PhD in 1988 from Harvard University.
Congress president Sonia Gandhi also congratulated the Indian-origin economist, besides Duflo and Kramer, while party leader Rahul Gandhi said Banerjee helped the Congress conceptualise its 'Nyay' scheme.
'Apart from making the nation of his origin proud by this spectacular achievement, Prof Banerjee's and his fellow recipient's work in 'experimental approach to alleviating global poverty' had helped millions across the globe, including India, come out of poverty.
'Their methodology, approach and experiments were exemplary and of extreme contemporary relevance. His recognition as a Nobel laureate has delighted every Indian,' Sonia Gandhi said in a statement.
Congratulating Banerjee, Rahul Gandhi said he had helped the party conceptualise its 'Nyay' scheme to help remonetise the economy.
'Congratulations to Abhijit Banerjee on winning the Nobel Prize in Economics. Abhijit helped conceptualise NYAY that had the power to destroy poverty and boost the Indian economy. Instead we now have Modinomics, that's destroying the economy and boosting poverty,' he said on Twitter.
Congratulating Banerjee, former prime minister Manmohan Singh said his work on poverty alleviation and development of new techniques were truly path-breaking.
He said Banerjee's pioneering innovations in development economics were applicable and useful to policy making in developing countries such as India.
In a letter to Banerjee, Dr Singh said, 'It gives me immense pleasure and pride to know that you are now the second Indian to receive the Nobel Prize in Economics.'
'My heartiest congratulations to you and your co-winners. Your scholarly work on poverty alleviation and development of new techniques such as Randomised Control trials are truly path breaking,' Singh, a renowned economist himself, added.
'I am particularly pleased, as a student of economics, that the Committee chose to honour pioneering innovations in development economics that are very applicable and useful to policy making in developing countries such as India,' the senior Congress leader said in his congratulatory message to Banerjee.
The Congress party also tweeted, saying, 'Congratulations to Abhijit Banerjee for winning the Nobel Prize 2019. His incredible work in poverty alleviation has made our country proud. The renowned economist was a key consultant for the path breaking NYAY programme presented by the Congress party.'
Congress leader and former Union minister Jairam Ramesh also tweeted, saying, 'Delighted that Abhijit Banerjee and Esther Duflo have won this year's Economics Nobel. As Minister of Environment and Forests in 2010, I had asked Duflo to work on market instruments for pollution control. I'm glad that system is now in use in Gujarat.'
Flashback: The Indians who have won the Nobel
Happy and proud: Abhijit Banerjee's mother
Abhijit Banerjee joins list of Indian Nobel Laureates
Abhijit Banerjee, the desi who won Nobel in economics