Stuttgart survived a relegation scare for the second consecutive season with a 2-1 win over Paderborn on Saturday.
The 61-year-old, who took over the struggling side in November, completed a similar feat last year after taking charge in March.
“Huub Stevens is the coach of the century for a different club but for us, he is the rescuer of the century,” director of sport Robin Dutt told the players at their final gathering on Sunday.
Schalke fans voted Stevens as their coach of the century after leading the side to UEFA Cup success in 1997 and the Dutchman has also worked at Hamburg SV, Hertha Berlin and Cologne among others.
But the club have quickly confirmed that Stevens will again be leaving despite rescuing the former Bundesliga champions from the drop.
“For Huub Stevens this was the farewell as his contract ran out and the Dutchman will not be on the Stuttgart bench next season,” a statement from the club read.
Stuttgart confirmed they had informed Stevens of their decision to find a new coach some time ago but officials opted to avoid telling the team so as not to distract them during the fight against relegation.
Former Leipzig coach Alexander Zorniger has emerged as the front-runner to succeed Stevens in the German media.