Touré scored his second European goal on 19 April 2006, the winner in the first leg of the Champions League semi-final against Villarreal CF. It was the final European goal scored at Highbury and the goal that effectively decided the tie (Arsenal won 1–0 on aggregate), to send Arsenal through to their first ever Champions League Final, in Paris, France.
Touré was handed the number 5 shirt for the 2006–07 season, which had been vacant since the departure of Martin Keown. In August 2006, Touré signed a new four-year deal with Arsenal.
He was named in the 23-man squad taken by coach Henri Michel to the 2006 FIFA World Cup and made his first appearance in a FIFA World Cup on 11 June 2006 in the Ivory Coast's 2–1 loss to Argentina. He has scored three goals for the Ivory Coast to date, two of them headers against Guinea and Gabon one against Japan, a 20-yard shot from outside the penalty area that flew into the top corner of the goal.