Sri Lankan Prime Minister Ranil Wickramasinghe was present at the airport to see-off Modi.
On the last day of his five-day three-nation tour that also took him to Seychelles and Mauritius, Modi became the first Indian Prime Minister to visit Jaffna.
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.
The first Prime Minister to visit the island after Rajiv Gandhi's trip in 1987 following which the bilateral relationship had undergone several twists and turns, he said the two nations should build a climate of trust and confidence while remaining sensitive to each other's interests.
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He addressed the Sri Lankan Parliament and held talks with the top Lankan leadership, including President Maithripala Sirisena, during his visit.
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.
Modi's final destination was Sri Lanka and during his trip to the islanad, Modi visited Colombo, Sri Lanka's ancient capital Anuradhapura, Talaimannar and Jaffna.