The referee, Cesar Flores, 48, was killed after being shot three times – once in the head, neck and chest, according to the police.
The player, who is at large, also wounded another player, 25-year-old Walter Zarate, before fleeing the scene.
The incident happened in the Cordoba district of Argentina after Flores showed the footballer, a straight red card earlier in the match after he hit one of the opposition.
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“It all happened during the match,” said a police spokesman. “We don’t know what happened with the referee but the player was angry and went to get his gun and killed him.”