The fishermen were handed over to the Indian Coast Guard Ship "Rajkamal" at the seas off Mannar, Sri Lankan Navy said in a statement.
"Under the direction of the president steps have been taken to repatriate 33 Indian fishermen in the Sri Lanka custody with the immediate effect on June 5," the statement said.
In New Delhi, External Affairs Ministry spokesperson Syed Akbaruddin tweeted, "Yes 33 fishermen have been released by Sri Lanka and handed over to Indian Coast Guard today afternoon."
The 29 fishermen, with four others, strayed into Sri Lankan waters on June 1 after their boat developed a technical snag.
President Rajapaksa's order to release fishermen is to signify a goodwill gesture by him to the new Indian government, his spokesman had said.
Rajapaksa had attended the swearing in ceremony of Prime Minister Narendra Modi on May 26 in Delhi.
He had ordered the release of all Indian fishermen in Sri Lankan custody last month.
Sri Lanka had shot down a request from Tamil Nadu fishermen to allow fishing in Lankan waters for 70 days a year and to allow bottom trawling.
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