But Waris fought restored parity for Lorient in the 72nd minute before Jimmy Cabot doubled the advantage for the Oranges.
Waris then sealed the win with a late strike in the 90th minute.
The striker has now scored six goals for Lorient this season.
The player was snubbed by Black Stars Coach Avram Grant for the Africa Cup of Nations in Gabon.
His performance will raise further questions to what led to his exclusion from the Ghana team.
New signing Alhassan Wakaso could only watch the game from the bench for Lorient.