He made his professional regular-season debut during the Saints' season-opener at the Cleveland Browns and recorded three combined tackles during their 19–14 victory. On September 25, 2006, Ninkovich suffered a torn MC ligament in his knee while appearing on special teams during the Saints 23–3 victory over the Atlanta Falcons on "Monday Night Football". On September 29, 2006, the Saints placed Ninkovich on season-ending injured reserve after he underwent surgery to repair the torn ligament. Ninkovich finished his rookie season with four combined tackles (two solo) and a pass deflection in three games.