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."
FLAMBOYANT PROCESSIONS
Nearly 1,500 policemen were on duty for the game. Several hundred police and firemen packed the athletics track around the pitch more than an hour before kick-off.
Police also used horses, dogs and specialised equipment to tackle public order offenders.
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.
Violence continued outside the stadium as CSKA fans again clashed with police, who made more arrests.
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.
The two teams finished with 10 men after Levski midfielder Hristo Yovov and CSKA winger Alexander Tonev were sent off with 20 minutes remaining.
CSKA have 29 points from 16 matches. Levski remain second on 32, five points behind leaders Litex Lovech.
