Cheick Diabate ensured Newcastle will have to take their chances in the draw for the knockout stages as Bordeaux finished top of the group.
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 their 3-0 loss at St James' Park in October.
It was little more than the French side deserved. 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 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.
"We wanted to qualify and we did that with a game to spare," said Pardew. "We can look forward to February. I am just hoping that when we come out of the other side of the (transfer) window, we have got a stronger squad."