Brest dropped to the bottom of Ligue 1 following a 2-1 loss at Montpellier.
Troyes' 1-0 victory at home to Evian saw Brest slip six points adrift of 17th-placed Nancy, who face Lyon on Sunday, with just three games of the season remaining.
Marco Estrada opened the scoring for the home side but Florian Raspentino quickly equalised before Souleymane Camara's second-half penalty handed Montpellier victory.
The outgoing champions took the lead after just 12 minutes as Remy Cabella found Estrada. The Chilean midfielder sprinted past Abdoul Sissoko and then unleashed a shot from 25 yards which gave Alexis Thebaux no chance.
But the lead lasted only nine minutes as Brest stunned the hosts on the counter attack.
Estrada's corner was gathered by Raspentino who charged up the field and exchanged passes with Charlison Benschop before firing past Geoffrey Jourdren from distance.
Montpellier could have gone back into the lead just before the half-hour but Thebaux made a good save from Estrada.
Camara then clipped the post with an effort six minutes after the break but Benoit Lesoimier should have given Brest the lead three minutes later as he found himself one-on-one with Jourdren, but the keeper made a fine save.
And with 17 minutes to go the visitors were made to pay as Ahmed Kantari felled Daniel Congre in the penalty area and Camara dispatched the spot-kick to Thebaux's left.
Cabella had the chance to put the match to bed in the 83rd minute but Thebaux was on hand to turn his speculative shot away.