On the back of a three-game losing run, Stephane Moulin’s men halted the poor form with the Cameroonian playing a key role in the tie.
Bahoken opened the scoring five minutes into the game after benefitting from Flavien Tait’s assist to set his side on the path to victory.
However, in the 89th minute, substitute Waris levelled proceedings for the hosts, profiting from top scorer Emiliano Sala’s assist
Bahoken who was cautioned in the 36th minute featured for the entire duration of the tie along with Senegal international Cheikh Ndoye and Cote d'Ivoire defender Ismael Traore.
The summer signing has now scored four goals since his switch from Strasbourg while Waris has two in 15 appearances.
With the result, the Stade Raymond Kopa outfit are 13th in the log with 16 points from 14 games while Nantes are 10th with 17 points from the same number of matches.