In 2005, Emerson won the 2005 Confederations Cup with Brazil, who defeated South American rivals Argentina 4–1 in the final, as well as overcoming hosts Germany 3–2 in the semi-finals. On 30 March 2005, Emerson scored a goal in an away 1–1 draw against Uruguay in a 2006 World Cup qualifying match. In the 2006 World Cup, he played in three of Brazil's five matches at the tournament, appearing in Brazil's two opening wins over Croatia and Australia during the group stage, while he was rested in the final group match against Japan, which Brazil won 4–1. He also appeared in Brazil's 3–0 round of 16 victory over Ghana, although he was taken off in the 46th minute after sustaining an injury. This would be Emerson's final match for Brazil. Brazil were eventually knocked out in the quarter-finals by eventual finalists France. Emerson was excluded from the starting line-up in Brazil's quarter-final match due to injury.