Luiz Moraes de Souza, 27, said he assaulted the referee, Jordan Silva, 20, but did not take part in killing the man.
Police in Pius XII in Maranhao State said they are looking for two other people who may be responsible for killing Silva.
City police said the altercation took place last week during a game when Silva called a penalty on player Josenir Santo Abreu. The referee gave him a red card -- the highest penalty -- ejecting the player from the game.
Abreu, 30, confronted the referee, kicking and striking him, police said.
Silva pulled a knife on Abreu and plunged it into his chest, the police statement said. Abreu was rushed to a hospital, but died en route, CNN reported.
Meanwhile, fans and family members of Abreu grabbed Silva, tied him up and tortured him. Upon learning Abreu died, the mob stoned Silva to death and cut his body into pieces, the statement said.
The perpetrators put Silva's head on a stake, Brazil's R7 News reported.
Investigators are using cellphone footage of the incident to identify those responsible for the slaying, CNN said.