Cheick Diabate ensured Newcastle will have to take their chances in the draw for the knockout stages of the Europa League as Bordeaux finished top of Group D.
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The Mali international striker headed home Fahid Ben Khalfallah's 29th-minute cross and then slid a 72nd-minute shot through keeper Rob Elliot's legs to condemn the Magpies to a first European defeat of the season and avenge for their 3-0 defeat at St James' Park in October.
It was little more than the French side deserved as despite manager Francis Gillot making the same number of changes as Alan Pardew, they enjoyed the better of the game apart from a brief flurry at the start of the second half.
But for Elliot, who made important first-half saves from Henri Saivet, Ben Khalfallah - who passed up a glorious opportunity at the death - and former Sunderland strike David Bellion, they could have won even more handsomely in front of a crowd of 19,983 at the Stade Chaban-Delmas.
Newcastle, whose arrival in France on Wednesday night was delayed by almost four hours because of snow on Tyneside, needed a victory to snatch top spot back from Bordeaux, but they rarely looked like securing it as few of the youngsters handed a chance to shine managed to do so.
With the two sides having already qualified for the knockout stages and both managers admitting they were not sure how much an advantage finishing top of the group would be, it was no surprise when they made wholesale changes.
Only Mike Williamson and Sylvain Marveaux survived from the Magpies' 3-0 Barclays Premier League victory over Wigan on Monday evening, and that meant starts for James Tavernier, Shane Ferguson, Gael Bigirimana, Mehdi Abeid, Sammy Ameobi and, for the first time since April 2010, striker Nile Ranger.
Like Pardew, Gillot made nine changes, one of which handed Bellion a chance to renew hostilities with his one-time employers' neighbours.
The Newcastle boss had admitted in the run-up to the game that his side might have to try to hang on until late into the game before launching their bid for victory, and they started in exactly that mode.
Indeed, they did not muster a single attempt on goal of any note as front three Shola and Sammy Ameobi and Ranger were starved of meaningful possession.
Pardew's team may have been makeshift, but so too was Gillot's.
However, the Frenchmen played with a panache which pinned the visitors back for long periods and had it not been for Elliot, they could have been out of sight before the break.
He was called upon for the first time with less than two minutes gone when midfielder Saivet was allowed to control skipper Gregory Sertic's corner and shoot from close range, the keeper getting a vital touch to send the ball over the bar.
Dangerman Ben Khalfallah tested him from distance nine minutes later, and he had to get down well to keep out Bellion's fizzing 18th-minute shot on the turn with Diabate failing to make the most of the rebound.
But there was little Elliot could do to repel Bordeaux with 29 minutes gone when Bellion and the excellent Ben Khalfallah combined down the left for the latter to curl an inviting cross into the box.
Diabate gave Williamson the slip to climb high above James Perch and direct a firm header past the helpless keeper.
The Magpies had been largely content to try to hit their hosts on the break, but got little change until three minutes before the break when Sammy Ameobi raced from his own half and played the ball into the path of older brother Shola.
He fed it inside to Ranger, but in a slip symptomatic of his team's first-half display, he failed to collect the ball and the attack was over.
The younger Ameobi's departure at the break saw Vurnon Anita step into a reshaped midfield with Ranger and Shola Ameobi in attack, and the change almost paid dividends within two minutes when the latter got to his strike partner's knockdown ahead of keeper Kevin Olimpa, but could only toe poke the ball wide.
Ameobi did force Olimpa into a crucial save five minutes later after Bigirimana had picked him out with an excellent cross, and the keeper was relieved to see Mehdi Abeid's curling 54th-minute effort drop just wide after sailing over his out-stretched arm.
Diabate sliced well wide under pressure from Williamson and Sertic only just missed from distance as the home side responded, but hopes of a fightback were dashed with 18 minutes remaining when Diabate ran on to Andre Poko's ball over the top and beat Elliot to wrap up the win.
Newcastle could now find themselves pitched into battle with one of the Champions League drop-outs when the competition resumes in the new year, and that would be an all together different challenge.