The defender went down clutching his left foot after attempting a clearance in the 40th minute and had to be stretchered off at the Valley.
Head Coach Martin Jol reported: "Goran has broken the second toe on his left foot so he will be out for a few weeks. It's very unfortunate for him."
He knew straight away that he'd done something. It's disappointing for him
Reserve coach Clive Allen added: "It was an unlucky one - the ball was on the edge of the area, Goran went to clear, kicked the ball and then kicked the bottom of the opponent's boot.
Goran Bunjevcevic faces a spell on the sidelines after breaking a toe in last night's reserve draw at Charlton.