Les Gones secured a 3-1 triumph on Sunday night and moved up to fourth place in the Ligue 1 table, as they look to reach next season's Champions League via one of the two routes.
Coach Paulo Fonseca made five changes to the team on duty against the Reds, including resting three of the four starting defenders, and yet still managed to gain the three points.
Georges Mikautadze and Rayan Cherki, scorer of the late equaliser in the first leg, were in fine form to help propel the visitors to victory.
As Alexandre Lacazette had a goal ruled out for offside and twice went close with other efforts, the first half remained goalless.