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Nene was denied by a combination of Benoit Costil and the woodwork after 18 minutes, but the same player found the equaliser just two minutes later. Javier Pastore sent the Brazilian through, allowing him to chip the ball over the onrushing Costil.
Costil's day went from bad to worse minutes later as he came out of goal to act as a sweeper, only to bring Jeremy Menez down leaving the referee no choice but to send him off.
Rennes didn't let their numerical disadvantage hamper them, however, and retook the lead in the 35th minute through a fine Feret free kick.
Nene almost levelled the sides for the second time in the match during first half stoppage time, but his curling effort was well saved by sub keeper Chieck N'Diaye.
That was Makoun's penultimate action in the game, however, as he received a second yellow shortly after to reduce Rennes to nine men.
N'Diaye was called upon to make a string of magnificent saves in the closing stages as Rennes held out for a famous victory over the league leaders.