The powerful explosion came just hours after President Mahinda Rajapakse announced the army's capture of the Tamil Tiger rebels' political capital in the north of the island.
"Two airmen died in the suicide blast and another 14 airmen were wounded," hospital spokeswoman Pushpa Soysa told AFP.
"Another 22 people, all civilians, were also wounded and admitted to hospital."
Police said the bomber tried to enter the airforce base but was stopped by sentries.
Most of the civilians were bus passengers whose vehicle was passing the gates of the facility, located opposite a luxury hotel.
There were no reports of foreign nationals among the wounded, the hospital said.
The attack came as security in the capital was stepped up after the announcement that the Tigers' political headquarters, Kilinochchi, had fallen to the army.
The president of the Maldives, Mohamed Nasheed, was also visiting Colombo at the time of the blast, officials said, adding that some of the streets in C