Media reports said around 100 people were injured in Sunday's game between Sport Huamanga and Sport Huancayo in the Andean city of Ayacucho.
Television showed dozens of fans breaking down fencing, invading the pitch and overturning a vehicle which appeared to be an ambulance.
Pictures also showed a police car in flames while referee Alejandro Villanueva told the El Comercio newspaper he was trapped in the stadium for nearly three hours.
Huamanga won the Copa Peru tie 4-1 but were beaten on away goals.
The trouble started when Huancayo were awarded a free kick as the hosts pressed for a decisive fifth goal.
The referee was surrounded by furious Huamanga players and needed protection from riot police, delaying play for nine minutes.
Play resumed but fans started throwing stones on to the field, forcing the game to be abandoned.
TEAR GAS
Fans then broke down the fencing and an estimated 200 people invaded the pitch while the police, heavily outnumbered according to the reports, used tear gas to try and control the situation.
Television showed police protecting the visiting team and a member of the Huancayo coaching staff lying injured on the turf.
The Copa Peru involves mainly semi-professional teams and rewards the winners with a place in the top flight the following year.
Peruvian soccer is in a chaotic state and riots and fighting are common at matches.
Last week Peru were suspended from international competition by ruling body FIFA because of a row between the national soccer federation and the government.
