Trains connecting Aswan to the High Dam station resumed on Monday after a one-day stoppage, said railways authority head Samir Nawar.
Trains linking Aswan to the capital are still suspended.
On Sunday, train movement between Aswan and Cairo was halted, and 17 local schools and Aswan University were closed, following renewed tribal clashes that left another two killed, raising the death toll to 25 since Friday.
The fighting began on Wednesday between an Arab clan, Bani Helal, and a Nubian tribe, Daboudiya, over the harassment of a girl and offensive graffiti written on the wall of a school by students from the feuding families.
On Friday, tensions escalated into violence, beginning a three-day battle.
It remains unclear who was responsible for starting the violence.