Born in Rijeka, Knežević started his professional career with the city's First League side NK Rijeka in 2002 and subsequently made 115 appearances in the league before moving to Livorno on a three-year deal in late August 2006.
He made his Serie A debut on 25 October 2006 in Livorno's 4–1 defeat to Internazionale and scored his first goal in the league against Cagliari on 18 April 2007 to secure his team a 2–1 victory.
On 30 June 2008, Juventus has swooped to sign Knežević on a season-long loan deal worth €750,000, with the option to acquire half of the contractual rights at €1.6 million following Livorno's relegation to Serie B.
In the 2011–12 Serie B season, Knežević again made 31 appearances in all competitions as the side narrowly avoided relegation.
He assumed the captaincy and led the club to a third-place finish in 2012–13, missing just two games all season.