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Etienne started the fixture positively and they almost went in front when Romain Hamouma broke through on goal, only to be thwarted by the out-rushing Boulogne keeper.
The Greens were almost in again in the 15th minute, this time as Yohan Mollo tested the home keeper with a strong shot from the edge of the box.
Etienne were given a real shock in the 75th minute of the game when Boulogne were handed a penalty as Ruffier was adjudged to have committed a foul in his own area, much to the dismay of his teammates.
With an upset on the cards, Soubervie made no mistake from the spot with a kick that edged past the incensed Greens stopper to make it 1-0.
The lead was not to last too long, however, as Benjamin Corgnet restored parity in the 84th minute with a deflected header from Mollo's free kick to force extra time.
Etienne came close to wrapping things up in the additional period when Melvut Erding combined with Mollo, before being thwarted in front of goal by the Boulogne stopper, who pushed proceedings into a shootout.
Following a tense close to the game, Christophe Galtier's side finally won out with a 4-3 victory on penalties.