Hundreds of policemen, wearing helmets and using batons, entered the CSKA supporters' section at the Georgi Asparuhov Stadium and forced them to leave.
They escorted them to the city's downtown area, where there was further trouble after the match, with minor fighting and buses, cars and shops damaged.
Television footage showed several fans with serious wounds taken to hospital by ambulance. Several local media described one supporter's condition as life-threatening.
The match continued after the halftime interval with the CSKA fans' section empty. Both sides had a man sent off as CSKA won 3-1 to move up to fifth in the Bulgarian league.
The violence was amongst the worst in recent years at the "eternal derby", as matches between Levski and CSKA are known, and confirmed the worst fears of police, who wanted an earlier kickoff because tensions were running high beforehand.
"They (CSKA fans) broke all safety fences and there was a possibility of a pitch invasion," Sofia police chief inspector Anton Zlatanov told local radio.
"We had no choice (but to enter the CSKA section). They threw concrete and iron pieces, injuring several policemen." CSKA fans also pelted police with fireworks.
CSKA's national fan club chairman, Dimitar Angelov, told reporters: "We want to meet Interior Minister Tsvetan Tsvetanov.
"We respect the law and the Bulgarian police but it's not acceptable for 3,500 fans to be pushed outside the stadium because of the misconduct of two or three... our fans broke a few seats because they're smeared with excrement."
Trouble began hours before the match with police making several arrests as the supporters of both teams made flamboyant processions through some of Sofia's main streets.
CSKA's win was only their second at the Georgi Asparuhov stadium. Brazilian striker Michel Platini scored twice and defender Apostol Popov made it 3-0 midway through the second half. Levski's consolation was a Kostadin Stoyanov own goal.
