The Swiss star was interviewed on live television after the 2-0 victory against Northern Ireland when a man stormed forward and hung a jacket with the Kosovo Liberation Army KLA emblem on him.
The incident has attracted a great deal of attention in neighboring Serbia, which has never recognized Kosovo's independence.
According to the Swiss Confederation, the man has been arrested and given a restraining order from the Stade de Genève match arena.
"It is unacceptable to use football stadiums, and in this case a television interview after the match, to spread political propaganda," the association said in a statement.