Hosts Lyon, hoping to make the last four of European club football's premier competition for the first time, opened the scoring through Lisandro but were pegged back minutes with a splendid goal by Morocco striker Marouane Chamakh.
Lyon made it 2-1 courtesy of Brazilian winger Michel Bastos around the half hour and a Lisandro penalty 13 minutes from time gave them a significant advantage over French champions Bordeaux, who ended Lyon's seven-year reign at the top of Ligue 1 last year.
Bordeaux have the edge over Lyon in Ligue 1 this season but the home side, who have reached the quarter-finals three times before, showed their greater Champions League experience.
Those who feared a tight, tactical affair on the Gerland pitch were soon reassured when, after a poor clearance from the Bordeaux defence, defender Mathieu Bodmer sent a low cross that Lisandro deflected into the net to open the scoring.
TOPSY-TURVY ENCOUNTER
Bordeaux replied almost immediately, France playmaker Yoann Gourcuff sprinting down the right to deliver a perfect cross for Chamakh to superbly head home the equaliser four minutes later.
Lyon came close to a second goal on 25 minutes, winger Cesar Delgado racing into the box unchallenged only to shoot straight at Bordeaux keeper Cedric Carrasso.
Seconds later it was Bordeaux's turn to have a great opportunity when Yoan Gouffran forced a good save out of France keeper Hugo Lloris.
Lyon were soon back on top by winning the fierce midfield battle and constantly racing the ball forward, though they were helped by more poor defending from Bordeaux.
After a fine solo run Bosnia midfielder Miralem Pjanic crossed for Bastos, who latched onto the ball after a missed header and left Carrasso no chance by firing high into the net on 32 minutes.
The second half was tighter with spells of pressure from Bordeaux but they were denied by Lloris, notably from a spectacular Chamakh volley on the hour.
Lisandro, who kept fighting and symbolised Lyon's determination throughout an exciting contest, fittingly put the issue beyond doubt from a spot-kick after Bordeaux defender Matthieu Chalme was unlucky to be penalised for handing the ball in the area following Aly Cissokho's speculative shot.
Lyon will be without Lisandro and forward Sidney Govou for the second leg next Wednesday after the pair picked up yellow cards.
The winners face Manchester United or Bayern Munich in the semi-finals to try to become the first French club to play the Champions League final since Monaco lost it to Porto in 2004.
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