"We have different opinions regarding CSKA's main goals, especially concerning the league title," the club's chairman Dimitar Borisov told reporters.
"We want the title but he couldn't guarantee he would be able to fulfill this task."
CSKA went into the winter break second in the standings with 31 points from 15 matches, four points behind Litex Lovech.
CSKA said all Penev's assistants had been released and junior team coach Adalbert Zafirov would take training at the club's first session of the year on Thursday.
Former CSKA coach Miodrag Jesic, who won the league title with the Sofia-based club in 2005, has emerged as the favourite to take over after Penev's resignation.
CSKA said they are holding talks with the 51-year-old Serb, currently with Libyan league leaders Alittihad, who has also coached Slavia Sofia and Litex Lovech in Bulgaria's top flight.
"We're talking to three coaches but Jesic is one step ahead," said Borisov.
Penev tried to quit last November after a disagreement with the club's owners over their decision to reinstate nine suspended players but CSKA refused to accept his resignation.
Penev, who scored more than 150 goals in the Spanish league for Valencia, Atletico Madrid, Compostela and Celta Vigo, replaced his uncle Dimitar at CSKA last March and guided them to the second place in the championship.
Crowd favourite Penev recorded 25 wins, seven draws and 10 defeats in 42 matches in all competitions during his 10-month spell at the 31 times Bulgarian champions.
