The 25-year-old headed home on the stroke of half-time as Remi Garde's men slipped further adrift of the Champions League places
Yoan Gouffran scored the decisive goal, nodding home a Ludovic Obraniak corner just before the break, and although Remi Garde's men had large spells of possession after the interval, they were unable to find an equaliser.
The game got off to an inauspicious start as Bafetimbi Gomis forced a save from Cedric Carrasso with a tame shot from the edge of the area.
An unmarked Michael Ciani then nodded a set-piece wide, before a moment of individual brilliance created the first goal.
Nicolas Maurice-Belay went on a fantastic run down the right, leaving the Lyon back line in his wake, before cutting the ball back, only for Anthony Reveillere to send it out for a corner.
Obraniak's delivery took a cruel touch off Bakary Kone and fell perfectly for Gouffran, who powered a header into the roof of the net, evading Reveillere who was well-stationed on the line.
Lyon soon had the ball in the home side's net, but the referee rightly ruled Kim Kallstrom offside in the build-up, ensuring Bordeaux went into the break a goal up.
Rather than coming out from the interval reinvigorated, Lyon looked static in the early exchanges of the second period.
Mariano had a threatening cross well held by Hugo Lloris with a host of Bordeaux attackers looming, before an excellent piece of defending from Reveillere forced Gouffran wide as the 25-year-old latched on to Obraniak's through ball.
Benoit Tremoulinas combined twice in quick succession, with Obraniak sending one shot over, before narrowly missing a beautiful delivery from the 26-year-old.
Obraniak was involved again with another free kick, however an unmarked Ciani skied the ball when he should have done better.
However, as time ran out, Lyon began to threaten more. Jimmy Briand had a credible appeal for a penalty turned down, before Ciani and Marc Planus denied Lisandro Lopez and Gomis in quick succession, closing down the OL attackers.
A tame Briand effort forced a rare save from Carrasso, before the former Toulouse goalkeeper had to be alert to stop Ciani's interception from running into his own net.
At the other end, Bordeaux continued to look the more threatening of the two sides. Lloris kept his team in the contest, brilliantly tipping over Jaroslav Plasil's free kick, before Ciani sent the resulting set-piece wide.
Ederson sent a free kick straight into the wall deep into stoppage time, before the referee ended the match.
The defeat leaves Remi Garde's men in fifth place, three points adrift of Lille, who have played one less game.