João Rodrigo Silva Santos, 35, was a forward for a number of mostly second-tier Rio de Janeiro football teams before retiring and opening a health foods store.
Police said that Mr Santos is believed to have been snatched as he closed up his shop in Rio on Monday night.
Witnesses said they saw several men bundling him into his car and speeding off just before midnight.
Mr Santos' brother-in-law 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."
Mr Santos' eyes and tongue had been gouged out, according to Brazilian media reports.
Investigators are looking into whether Mr Santos was murdered by a drugs gang because of Ms Silva's work at a military police base in a local slum.
One police official told Brazil's O Globo newspaper that authorities are also investigating whether a recent post on the store's Facebook page could be connected to the crime.
The post showed surveillance footage and asked for help catching shoplifters.
some sick wicked pple out there
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