Fifa's own video of the incident in Portugal's final group game against South Korea showed Joao Pinto striking the official.
The 30-year-old Sporting Lisbon forward has been suspended from "all match activity" until the world governing body looks into the matter further and decides what punishment to take.
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Players always run the risk by laying hands on the referee
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Fifa's Keith Cooper
A Fifa statement said that the evidence already in its possession indicates that Pinto "when shown the red card, punched referee Angel Sanchez, of Argentina, in the stomach".
That evidence came from the reports submitted by the referee of the match, the match commissary and the referee inspector, Fifa said.
"The act of hitting a referee is considered to be a serious violation of the Disciplinary Code.
"Given the serious nature of the offence of which the player is accused and in order to take a decision in full cognizance of all facts, the disciplinary committee has already requested additional information."
The incident during Thursday's game was not seen on television broadcasts.
New light
But a Fifa source said one of their cameras near the corner flag clearly shows the refereeing flinching from Joao Pinto's punch.
"There are video pictures from another camera which have shed new light on the incident," Fifa communications director Keith Cooper told a news conference.
"The general rule is that the referee should not be touched. Players always run the risk by laying hands on the referee."
It occurred in the aftermath of Pinto's red card for a bad foul on South Korea's Park Ji-Sung and could see him receive a lengthy ban.
Portugal captain Fernando Couto seems to have escaped punishment.
"He is not a factor in the equation," Cooper said.
The 1-0 defeat at the hands of the World Cup co-hosts knocked out Portugal, who host the European Championships in 2004.
Portugal defender Abel Xavier was banned for nine months for manhandling a referee as they exited the 2000 European Championship.
His ban was later reduced on appeal.