The 45-year-old has been in charge of the club since 2009, winning the Russian Premier League three times, including last season, as well as two Russian Cups and two Russian Super Cups.
CSKA have endured a disappointing campaign in UEFA's elite club competition but could yet finish third in Group E and qualify for the Europa League ahead of Tottenham, who they face at Wembley.
"CSKA thank Leonid Slutsky after seven years of fruitful co-operation, yielding three league titles, two Russian Cups and two Super Cups, as well as the incredible emotion that the team gave to our huge army of fans under his leadership over all these years," the club said in a statement.
"Our doors are always open to you, Leonid!"
He leaves with reigning champions CSKA third in the league table, ahead of the domestic season restarting in March with a home game against second-placed Zenit.
Slutsky also led Russia at Euro 2016 following the departure of Fabio Capello from the national team post in August 2015. However, they finished a disappointing fourth in Group B in France, behind Wales, England and Slovakia, prompting him to stand aside in June.