Thursday's 2-0 loss was CSKA's third in as many matches in Group L, leaving them bottom of the standings behind Porto, Besiktas and Vienna without a point or goal in the group campaign to date.
"We had no choice but to act after the negative results in the past weeks," CSKA president Dimitar Borisov told local media, adding that sporting director Emil Kostadinov would also vacate his post.
The match against Rapid was also marred by crowd violence as several hundred CSKA supporters clashed with riot police outside the Vasil Levski national stadium after the final whistle.
Angry fans, who have protested against the club management's policy on several occasions, threw plastic bottles, flares and other objects during the incident.
On Friday, Police said they had arrested 18 CSKA supporters while four policemen had sustained slight injuries.
Former Macedonia coach Jovanovski's departure means that CSKA will begin the search for an eighth coach this year and fourth since the start of the season.
Jovanovski, 54, took over from Pavel Dotchev nine weeks ago but could not produce a significant improvement in the team's results both domestically and in Europe.
The 31-times Bulgarian champions are ninth in the league standings on 13 points from 10 matches, 12 points behind leaders and city rivals Levski Sofia.
CSKA have yet to make an official announcement but former players Sasho Borisov and Milen Radukanov are expected to be taking charge of the side for the league match at Minyor Pernik on Sunday.
