At least three airmen were killed and 16 others wounded in the raid on the Katunayake airbase next to the airport north of Colombo, officials said.
A spokesman for the Liberation Tigers of Tamil Eelam (LTTE) warned of more attacks after the raid, which follows days of intense battles in the north and east of Sri Lanka that have forced tens of thousands of civilians to flee.
The Tigers were known to possess light fixed-wing aircraft and an airfield in the rebel-held northern Wanni region, but they had not used planes before in a combat mission.
The Bandaranaike international airport was not damaged but authorities temporarily shut it down as a precaution, reopening it after nearly three hours.
Aviation officials said that at least four inbound flights were diverted to India's southern city of Chennai as authorities sought to bring the situation at the base under control.
"One of the LTTE aircraft had flown over the airbase and dropped some explosive items," airforce spokesman Ajan