The man was left with half his left ear ripped off and bloodied in the incident, the Association of Chief Police Officers confirmed.
The incident happened before Uruguay and Liverpool striker Luis Suarez was banned from the competition for biting an Italian player but details of the attack have only just emerged.
Former Liverpool striker Stan Collymore tweeted that he had seen footage of the fan attack and claimed it would be "the biggest story in the UK, especially who did it".
Chief Superintendent Rachel Barber said: "We were made aware during the England vs Uruguay match in Sao Paulo that an incident had taken place which resulted in an England fan having a portion of his ear bitten off by another England fan.
"In the immediate aftermath, we managed to make contact with the victim and offered advice and support.
"The day after the attack, the victim chose to make a formal complaint to the local police, and they opened an investigation."
No arrests have been made yet but interviews with witnesses gave police a name for the alleged attacker, Ms Barber said.
Police went to England's final match against Costa Rica in Belo Horizonte in case the assailant travelled to the match but did not find him there.
A Foreign Office spokesman said: "We are aware of an incident in Sao Paulo on June 19 involving a British national and we provided consular assistance."