The attack was the third by Tamil Tiger aircraft since they carried out their first air strike last month when they bombed an air force base near Colombo, killing at least three airmen.
A soldier who witnessed the rebel attack, said he saw a low-flying aircraft drop two bombs on a gas storage facility in Kerawalapitiya, 10km north of Colombo.
The bombs started a fire, the soldier said, who spoke on condition of anonymity because he was not authorised to talk to the media.
The extent of damage was not immediately known.
Rasiah Ilanthirayan, a Tiger spokesman, said its aircraft bombed two facilities that supply fuel to the Sri Lankan air force.
"The two squadrons returned safely after the mission and the pilots have confirmed that they have hit the targets," he said by phone from the rebel stronghold of Kilinochchi.
As a security measure, officials knocked out power to the entire capital, as well as the country's only international airport and an adjoining air force base as the rebel aircraft approached.
The rebels have launched all three air raids at night, and fly without lights to avoid detection. Many people were watching Sri Lanka's cricket team play Australia in the World Cup final on television when the power was shut off.
Air traffic was suspended for about an hour, an employee of the international airport said, speaking on condition on anonymity.
Sri Lanka's separatist conflict flared in 1983 when Tamil Tiger fighters started fighting for an independent homeland for the country's 3.1 million ethnic minority Tamils, who complain of discrimination by the majority Sinhalese.
More than 69,000 people have been killed in the conflict.