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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.
Angry fans, who have protested against the club management's policy on several occasions, threw plastic bottles, flares and other objects during the incident.
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.
