Petkovic started off his career with South Melbourne and played for them from 1995-1999 playing over 100 games. In 1999 he moved to French side RC Strasbourg but didn't play a single league game and in 2000 he moved back to his old team South Melbourne. During his 2nd stint with the club he moved on loan to Lillestrøm a Norwegian club. In 2002 he moved to Turkish Super Lig side Trabzonspor and played 87 games for the club but left the club in 2005. He moved to Sivasspor and played 129 league games their and even managed to score a goal with the club. In 2010 he left the club to join A League side Melbourne Victory. He played over 25 games in his first a league season and looked to stay their for the next campaign. He looked to be 2nd choice goalkeeper for the next campaign as Perth Glory goalkeeper Tando Velaphi joined the Melbourne Victory. He announced his retirement from football shortly after the end of Melbourne Victory's Asian Champions League campaign.