Diego Armando Estacio, the second victim, was discovered in his car on Thursday evening by workers using a miniature camera.
The removal of the body may not be completed until Saturday.
Estacia, 19, was believed to have been sleeping in a car in the car park when the bomb exploded.
The other victim, Carlos Alonso Palate, 35, was found on Wednesday. His remains have been returned to Ecuador for burial.
The explosion brought down a multistorey car park at the recently opened Terminal Four building, burying the two Ecuadorean male victims under 40,000 tonnes of steel and concrete.
Saturday's attack brought an end to a nine-month ceasefire and the discovery of the caches of explosives has renewed fears that Eta might be planning a new campaign of violence.Eta's campaign for a Basque homeland has lasted for more than 40 years, during which more than 800 people have died.
Eta has not claimed responsibility for Saturday's blast, but a man who made a warning call to authorities before the explosion said he represented the group.
|Eta has been fighting for a separate Basque |
homeland for more than 40 years [AFP]
Jose Luis Rodriguez Zapatero, the Spanish prime minister, said that Saturday's attack would "achieve nothing, it is not going to intimidate anyone".
And his governing Socialist party acknowledged on Friday that the bombing showed that little had been achieved despite the ceasefire.
"We have to recognise that there was a problem of information and no dialogue," Jose Blanco, a senior Socialist Party official, told the radio station Cadena Ser.
"We have to analyse what happened to avoid repeating the same mistakes in the future," he added.
Zapatero announced in June that he believed the truce was sincere and said he would negotiate with Eta but the talks never got off the ground.
The government has rejected demands from Eta and its political wing, Batasuna, for preliminary gestures such as moving some prisoners to the Basque region and allowing separate talks among Basque political parties on the region's future.
Eta also has criticised the government for refusing to let up on the movement, citing the continued arrests of suspected members.
Despite the attack, Batasuna says peace talks with the Spanish government are not over.
Xabi Larralde, a Batasuna spokesman, said the peace process "is not broken".