The boy's father travelled to the Cordoba region from Dortmund to identify his son, whose body will now be examined in a post-mortem to find out how he died.
Local media reports suggest there is no sign of violence, and that it is expected that the boy, who has not been named, died of dehydration, heat exhaustion or a fall.
The boy's 40-year-old mother notified Spanish police that he was missing on Thursday, having shown up at a petrol station in a distressed condition, acutely dehydrated and covered in scratches and bruises.
She told police she had left home in Herdecke, North Rhine-Westphalia, to drive to Spain about a week previously, but was unable to say what had happened with her son.
Police found two rucksacks – one large, one small – and several empty bottles of water near the boy's body and are working on the theory that they suffered some kind of accident while hiking and that she left the child to go get help.
No records have been found of the pair having stayed in local hotels, and detectives believe they had been sleeping in their car, which was found on Tuesday near a religious shrine.
They had been seen on a fishing trip on Sunday, and had then asked for help on the Monday because the car had broken down.
The woman will remain in hospital until at least Monday.