There have been a number of car bombings this year
The controlled explosion, which damaged several vehicles and caused traffic chaos, came minutes after a caller claiming to be associated with the Basque separatist group ETA delivered a warning that an explosion was imminent.
ETA, which is blamed for about 800 deaths in its 33-year campaign for an independent Basque state, has vowed to attack tourist targets in Spain this year.
There have already been four car bombs on the coast.
A number of suspected Basque activists were arrested last week.
The BBC's Flora Botsford in Madrid says Monday's attack may have been intended to demonstrate that ETA is still capable of carrying out operations, despite the arrests.
The blast occurred in a multi-storey car park at about 0800 local time (0600GMT).
The structure was not damaged and no flights were cancelled, but travellers were forced to walk to the terminal with their luggage.
Security meetings
The explosion came as security chiefs were due to meet in the Basque capital, Vitoria, to discuss the ongoing operation against the Basque separatist group.
Spanish and Basque officials met last week amid fears that recent Basque separatist attacks are damaging Spain's lucrative tourist industry.
The talks were brought forward from the end of the month in an attempt to protect the tourist industry, worth $60bn a year, after a car bombing in the Mediterranean resort town of Salou on 18 August.
Thirteen people were injured in that attack - attributed to ETA - and extra police were deployed in popular resorts.
Security fears were heightened shortly before the meeting began on 20 August, when an explosion killed a 62-year-old woman in San Sebastian.
The blast was caused by a booby-trapped toy, but the attack did not appear typical of those usually blamed on ETA.
The Salou bombing, however, was seen as an ETA attempt to disrupt the Spanish tourist industry during the peak summer season.
Tourists targeted
ETA warned earlier in the year that it would target popular tourist destinations and warned travellers to stay away from Spain.
Seven attacks attributed to ETA have been aimed at key tourist areas.
In separate incidents in July, police defused a potentially devastating car bomb at Malaga airport on the Costa del Sol and a suspected ETA member blew herself up while handling explosives in the Mediterranean resort of Torrevieja.
Last year, Spain was the world's third most popular tourist destination - behind France and the United States - with more than 48 million foreign visitors.
And, despite the attacks, business is still booming in Spain's coastal resorts.
"The beaches are filled to the brim, the sun's out and the streets are as busy as ever," said Eduardo Moret, director of the tourist office in Salou.
The UK Foreign Office has played down the risks, but warned: "Visitors should be aware of the heightened level of terrorist activity directed against the tourist industry."