Elizondo was appointed to represent Argentina in the 2006 FIFA World Cup, together with fellow assistants Darío García and Rodolfo Otero. He officiated three group games: Germany vs Costa Rica, Czech Republic vs Ghana, and Switzerland vs South Korea. He also took charge of the England vs Portugal quarterfinal, as well as the final game between Italy and France, becoming the first referee in World Cup history to referee both the opening and final games of one World Cup, a feat later matched by compatriot Néstor Pitana in the 2018 edition (English referee George Reader also officiated the first and last matches of the 1950 FIFA World Cup in Brazil, but the last one, known as Maracanazo, was not technically a final). Elizondo handed out a total of 29 cards in the tournament, three of which were red, for an average of 5.8 cards per game.