Jovanović played for FK Rad in the Yugoslav First League during the 1987–88 and 1988–89 seasons. The next season, he transferred to the Greek side Iraklis Thessaloniki, where he played until the end of his career. During his spell in Iraklis, Jovanović evolved into one of the highest quality foreign players who ever played for the team.
On 18 June 2013, Jovanović was announced as the new head coach of the Emirati club Al Nasr, having signed a two-year contract. On 19 May 2014, Jovanović led his team to a 2–1 victory over Saham in the 2014 GCC Champions League final and won his first trophy as Al Nasr's manager.