In July 2005 he signed for Beroe Stara Zagora in the Bulgarian A PFG, for an undisclosed fee. On 7 August 2005, he made his league debut in a 3–1 away loss against Vihren Sandanski.
Džaferović scored his first ever goal for Beroe on 18 March 2006 against Litex Lovech; Beroe won 3–1. On 26 October 2006, Beroe manager Ilian Iliev chose Vanja as his club captain.