Wagner, who assumed the managerial reins at Cologne in March following Lukas Kwasniok's dismissal, helped steer his side to safety after they found themselves fighting relegation following a seven-game winless run prior to his interim appointment.
Claiming one win, three draws and three defeats from their final seven fixtures of the campaign, Wagner managed to guide the Billy Goats to a 14th-placed finish - a feat for which he has been awarded the job on a permanent basis, putting pen to paper on a deal which runs until 2028.
“René fits us very well because he not only understands the values of our club but lives them," said Cologne managing director Thomas Kessler. "Since he took over, he has shown that he can give direction in a difficult situation and bring people together for a shared goal.