The Top 14 team made it two wins and a draw in three games against their European pool rivals this season thanks to a flying start.
The win will give their new signing Ben Lam, who made his debut in the game, the chance to face the team coached by his uncle Pat at Ashton Gate, where Bordeaux’s former player Semi Radradra also plies his trade.
Edinburgh got off to a calamitous start in front of a 1,000 strong crowd at Stade Chaban-Delmas in temperatures that reached 28 degrees.
Fijian number eight Viliami Mata juggled and then dropped the kick-off and scrum-half Charlie Shiel’s clearance kick failed to find touch.
Bordeaux ran the ball back at their visitors and held onto it for a full two minutes. A knock-on eventually dented their hopes of scoring at the first attempt, but the first of their two tries in the opening 40 minutes was still on the board pretty quickly.
Edinburgh centre James Johnstone was brilliant stripped of the ball in a tackle by opposite number Ulupano Seuteni and the Samoan simply passed to Argentine flyer Santiago Cordero and he sprinted 40 metres to score.
Matthieu Jalibert added the extras and the home side, who were last in a European quarter-final as far back as 1997, made the perfect start.
Jaco Van Der Walt then shanked a routine penalty in the sixth minute to add to Edinburgh’s woes and a Shiel knock-on at the edge of the 22 then gave Bordeaux another chance to attack.
Marco Tauleigne picked up at the base of a powerful scrum and drove to within a metre of the line. A quick release allowed Jalibert to offload in a tackle in the shadow of the posts before sending centre Jean-Baptise Dubie over for a try that the outside-half converted.
Jalibert then pushed a 50-metre penalty inches wide and Bordeaux, who were sitting on top of the Top 14 table when it was cancelled last season, looked to be coasting.
But Edinburgh, showing seven changes from the side that had been beaten in the semi-finals of the Guinness PRO14 two weeks earlier, stayed in the fight and to their credit did not concede any more points in the half.
They finally got off the mark with a Van Der Walt penalty in the 31st minute and the South African outside-half cut the gap to eight points with a second penalty six minutes into the second half.
The Frenchmen hit back with penalties either side of a brilliant score in the corner by the visitors’ Damien Hoyland, which was made by fellow wing Darcy Graham.
Ben Botica confirmed the home win with a penalty from in front of the posts with the last kick of the match.
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