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Officials with Brazil's health regulator Anvisa walked on to the pitch at the Corinthians arena just minutes after kick-off to stop the game.
According to Anvisa, Argentina’s four Premier League players – Tottenham’s Cristian Romero and Giovani Lo Celso and Aston Villa’s Emiliano Martinez and Emiliano Buendia – are alleged to have declared false information on official forms to the country’s authorities and in doing so broken quarantine rules.
The players were surprised at the encroachment and the Argentines quickly left the field, although the two coaches, along with Argentina captain Lionel Messi and Brazilian players, gathered at the side of the pitch a few moments later to discuss the stop in play.
"Why did they start the game and stop it after five minutes?" Messi asked in comments heard on television. "We've been here at the stadium for an hour. They could have told us."
Messi returned to the dressing room and at 5pm local time, an hour after it began, the match was officially suspended.
“The referee and the match official will take a report to the Fifa Disciplinary Committee and they will decide what steps to take,” the South American Football Confederation said.
The incident occurred hours after Anvisa said four Argentine players must isolate and could not play in the match.
Under Brazilian rules, visitors who have been in the UK in the 14 days before entering the country must quarantine for 14 days on arrival.
Brazil’s health regulator was tipped off that the four did not give that information on their immigration forms and on Sunday said they confirmed their details were "false".
"Anvisa considers the situation a serious health risk and so has asked local health authorities to determine the immediate quarantine of the players, who are stopped from participating in any activity and should be prevented from remaining on Brazilian soil," the authority said.
But no action was taken and the four were allowed to travel with the Argentine team from the hotel to the Corinthians arena.
The confusion comes amid continuing anger in South America at rules that have robbed several teams of key players for this month’s three World Cup qualifiers.
Brazil are without nine key men for the Argentina game, and other South American sides have lost players due to a decision by some European clubs not to let their players travel to the continent.
They would have to quarantine on return and the clubs do not want to lose their players for league games.
Aston Villa said their players had agreed to return to their club after the Brazil game and miss Argentina’s match against Bolivia on Tuesday.
But the Argentine Football Association said they would play all three games.
Brazil lead the South American qualifying group for Qatar 2022, six points ahead of second-placed Argentina. The top four qualify automatically for Qatar.