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-Costa Rica, Czech Republic-Ghana, and Switzerland-South Korea. He also took charge of the England-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. 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. Elizondo took charge of the opening game of the tournament between Germany and Costa Rica, which Germany won 4-2. Elizondo handed out one yellow card, to Costa Rica’s Danny Fonseca. The match had a total of 22 fouls and 6 offsides, both statistics split evenly between the two teams. FIFA's president of the World cup organizing committee Lennart Johansson praised Elizondo performance at the match, saying "I did not notice him much which is a very good thing." In his following match, the Czech Republic 0-2 Ghana group game, he gave a straight red card to Czech player Tomáš Ujfaluši for a professional foulin the box, awarding a penalty to Ghana. He then gave a yellow card to Asamoah Gyan when he took the penalty kick prematurely. Gyan missed his second attempt. Elizondo also booked Czech player Vratislav Lokvenc and Ghanaian players Otto Addo, Michael Essien, Derek Boateng and Sulley Muntari, for a total of seven cards. He called 12 fouls against the Czech Republic and 20 against Ghana. He further ruled the Czechs offside 6 times and Ghanaians 9 times. Elizondo was also the referee in the Switzerland 2-0 Korea group game. Elizondo handed out nine yellow cards and no red cards during the match. He booked five Swiss players: Philippe Senderos, Hakan Yakın, Raphael Wicky, Christoph Spycher and Johan Djourou. The four Koreans to pick up cards were: Park Chu-Young, Kim Jin-Kyu, Choi Jin-Cheul and Lee Chun-Soo. Elizondo called 7 fouls against Switzerland and 19 against South Korea. There were a total of six offsides calls, split evenly between the two teams. He awarded the Swiss a goal when he overruled the assistant referee Rodolfo Otero's raised offside flag. Several players, including two defenders, Kim Jin-Kyu and Choi Jin-Cheul, who were following Alexander Frei stopped playing when they saw the flag. The ball was put into the path of Alexander Frei after being hit by Lee Ho's foot. Korea's coach Dick Advocaat was livid at the time, but a few days later agreed that the decision to allow the goal was correct. Elizondo was the referee in the England 0-0 Portugal quarter-final, which Portugal won 3-1 on penalties. Elizondo gave yellow cards to Ricardo Carvalho and Petit of Portugal and to Owen Hargreaves and John Terry of England, as well as a straight red card to England's Wayne Rooney after he stood on Ricardo Carvalho's groin, for a total of 5 cards. Elizondo called 18 fouls on England and 10 on Portugal, found Portugal offsides 3 times and England none.