Second-half goals by Ruben Baraja and Francisco Rufete turned the match around at the Stade Chaban-Delmas, after Les Girondins had taken the lead through Albert Riera in the first half.
However, the sending off of Bordeaux's Rio Mavuba for violent conduct became the turning point in the match, as the Spaniards eventually took advantage of the extra man.
Les Girondins started confidently and created the first chance of the match when Juan Pablo Francia shot just wide after a run from Mavuba saw him cut a pass back to the midfielder.
The French side broke the deadlock on 18 minutes, when Riera's low free kick from the right eluded Valencia goalkeeper Santiago Canizares at the near post, as the ball bounced in front and over the Spanish international for 1-0.
The goal sparked the match into life but it was English referee Mike Riley who become the centre of attention, as he issued five yellow cards and one red before the break.
On 27 minutes, the home side went down to ten men as Mavuba was sent off for lashing out at Valencia's Mohamed Sissoko.
Sissoko had brought Mavuba down in a challenge and while on the ground, the Bordeaux youngster kicked the Malian international in the head, though the French side claim it was accidental.
That gave the visitors the impetus to get back into the match with the extra man, but Bordeaux were able to take their lead into half time.
Valencia continued to struggle with attacks forward after the break, as Les Girondins held firm at the back.
However, the extra man would prove decisive in the latter stages, as Rafa Benitez's men would draw level with a quarter of an hour to go.
Baraja played a one-two with Sissoko, before striking his shot past Bordeaux keeper Ulrich Rame to make it 1-1.
That gave Valencia a precious away goal, but the Spanish Primera Liga title contenders would make the first leg safe when Rufete scored from the rebound after Nestor Canobbio's initial shot bounced back off the post.
The result gives Valencia the upper hand on their French counterparts, with the second leg at La Mestalla next Wednesday.
Click below for a match summary:
Uefa Cup quarter final, first leg
Bordeaux 1-2 Valencia
