Any game in the knockout stage that was undecided by the end of the regular 90 minutes, was followed by up to 30 minutes of extra time (two 15-minute halves). For the first time in an international football tournament, the silver goal system was applied, whereby the team who leads the game at the half-time break during the extra time period would be declared the winner.
If the scores were still level after the initial 15 minutes of extra time play would continue for a further 15 minutes. If the teams could still not be separated there would be a penalty shoot-out (at least five penalties each, and more if necessary) to determine who progressed to the next round.
The knockout stage began with the quarter-finals on 24 June and ended with the final on 4 July 2004 at the Estádio da Luz in Lisbon. Greece won the tournament with a 1–0 victory over the host nation Portugal.