The Billy Goats are yet to win in the Bundesliga from 14 attempts this term, leaving the club rock-bottom of the table and already a massive 11 points from safety as the midway point of the campaign approaches.
Stoger's last game in charge turned out to be the 2-2 draw away at Schalke on Saturday and the 51-year-old Austrian revealed he already knew his time was up before that contest.
"It was clear to us on Friday that the Schalke match would be our last," he told the club's official website. "We decided to wait until Sunday to communicate this in order to fully concentrate on the match. It is in the best interest of the club and especially the team that a decision was made and clarity restored.
"To the players, the staff at the club, the fans, and the city of Cologne: you have grown dear to the hearts of Manni Schmid [his assistant] and I, we will keep our fingers crossed that my successor manages to keep Cologne in the Bundesliga."