The horrified wife of Joao Rodrigo Silva Santos, 35, made the gruesome discovery as she left the house in Rio de Janeiro for work early yesterday morning.
The player's eyes and tongue had been cut out and his head placed inside one of his own rucksacks, police said.
Mr Santos retired from football two years ago after a successful career playing for several teams in Rio de Janeiro, as well as for clubs in Sweden and Honduras.
He had recently set up his own business selling health foods and dietary supplements.
Police said today that Mr Santos is believed to have been snatched as he closed up his shop late on Monday night.
Witnesses said they saw several men bundling him into his car, a Hyundai i30, and speeding off just before midnight, a spokesman said.
Mr Santos' brother-in-law, who didn't want to be named, told Brazil's Globo G1 website that the player's wife, Geisa Silva, 31, stayed up all night after her husband failed to arrive home.
He said: "Every time a car passed by she would go to see.
"She was getting ready to go to work at around 5.30am when she heard a noise, opened the front door and saw his rucksack. When she opened it, it was his head.
"From what I know, he didn't have any enemies and neither did his wife."
Investigators are probing whether Mr Santos was murdered by a drugs gang because of Ms Silva's work at a military police base in a local slum.
The 'Police Pacification Unit' in the Morro do Sao Carlos is one of dozens set up in Rio's favelas to retake control of the city's slums from violent drug traffickers.
However, according to police chief Rafael Rangel, Mrs Silva worked as a social worker in the base and didn't patrol the streets or make arrests like other police officers.
He told Brazil's O Dia newspaper the motives of the murder are still unclear.
He said: "Mrs Silva has no idea who would have done this.
"Neither she, her husband or any other member of the family have suffered any type of threat as far as she knows.
"There is nothing that would justify such a barbarous crime."
He added that police have begun searching for the rest of Mr Santos' body.
