The pair led Cologne back to the German top flight last season as they won the second tier by six points from Paderborn to end their two-year Bundesliga absence.
Cologne kick off their season on August 21 against Hamburg at the RheinEnergieStadion, with the club opting to secure their coaching team on contracts for a further two years.
Speaking at a press conference on Wednesday to confirm the agreement, Stoger said it was an easy decision for him to make.
"The last season was a lot of fun and we look forward to making the next steps in the future," he said.
"It will be an interesting season in the Bundesliga and we are looking forward to it. It was quite easy for us to extend the contracts."
Stoger has been busy in the transfer market since guiding Cologne back to the top flight, landing Chelsea defender Tomas Kalas on loan as well as signing Kevin Vogt, Yuya Osako and Simon Zoller.
"We have set up so that we can play both offensively and defensively. Our strength can again be our cohesion," he added.
