Claude Puel’s men hit the ground running in the encounter when Khazri opened the scoring in the 23rd minute after receiving a timely assist from Charles Abi.
Bouanga then doubled the lead in the 66th minute, firing in his effort from outside the box after he was set up Mahdi Camara.
Romain Hamouma found the back of the net for Saint-Etienne three minutes later but Video Assistant Referee ruled out the strike for offside.
Nimes had a glorious chance to reduce their deficit from the penalty spot with three minutes left to full-time but Renaud Ripart failed to beat goalkeeper Etienne Green.