Prabhakaran's son and heir apparent, along with the entire leadership Liberation Tigers of Tamil Eelam (LTTE), were killed, the defence ministry said.
"We have successfully ended the war," the island's powerful defence secretary, Gotabhaya Rajapakse, told his brother the president Monday in a nationally televised ceremony.
"Prabhakaran's body is among the 300 terrorist bodies that we captured," Army chief Lieutenant General Sarath Fonseka said on state television. "Now the entire country is declared rid of terrorism.
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The final battle marked the end of one of Asia's oldest and most brutal ethnic conflicts which left more than 70,000 dead from pitched battles, suicide attacks, bombings and assassinations.
Authorities had been determined to capture or kill Prabhakaran