In the second half of the 1976–77 season, Panajotović moved to fellow Yugoslav First League side Radnički Niš. He was a regular member of the team that reached the semi-finals of the 1981–82 UEFA Cup, scoring three goals in the process. During the following season, Panajotović left the club and spent the final years of his career with Yumco Vranje and Napredak Aleksinac, playing in the lower leagues.
