On the last day of his three-nation tour that took him to Seychelles, Mauritius and then Sri Lanka, Modi became the first Indian Prime Minister to visit Jaffna.
The special Air India plane carrying the Prime Minister and his delegation from Colombo landed here at 30 minutes past midnight.
The Prime Minister, who is also the second international leader to visit the once strife-torn region after Premier David Cameron in 2013, handed over 27,000 new homes to Tamils who became homeless during the civil war.
He also addressed the Sri Lankan Parliament and held talks with top Lankan leadership, including President Maithripala Sirisena, during his visit.
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Modi had started his trip on Tuesday when he reached Seychelles and held talks there, signing four agreements.
He then went to Mauritius where he met the leadership of the strategic Indian Ocean island. India and Mauritius signed five pacts during Modi's visit. The Prime Minister also addressed the country's National Assembly and attended a public reception.