The following season saw the arrival of Luciano Spalletti as Roma's new head coach. Under Spalletti's 4–2–3–1 formation, Perrotta played in a more advanced role, behind the first striker and in between the left and right winger as an attacking central midfielder, in which he was able to rediscover his form, becoming a key member of Roma's midfield, as Roma reached the 2006 Coppa Italia Final. In merit of his fine performances for the capital club, he earned a call-up to Marcello Lippi's Italy squad for the 2006 FIFA World Cup, starting all seven games for the eventual champions. In 2006, he also signed a contract extension with the capital club, keeping him in Rome until 2010.