After taking a second half lead through Nicolas Anelka on 60 minutes, an Alou Diarra header equalized for the home side in the 83rd minute.
After a drab first half, Frank Lampard managed to release Anelka through and the Frenchman opened the deadlock with a cool finish past Mathieu Valverde.
The Blues' pace slowed down after they took the lead, and Diarra did well to rise past John Terry and meet a left wing corner with a brilliant header.
The French side could have added a second, especially after Lampard was sent off for a second bookable offence four minutes from time.
After some anxious few minutes for Luiz Felipe Scolari's men, Chelsea managed to hold out for an away draw as they drop to second spot of Group A with eight points.
Qualification berths to the second stage are still up for grabs in the group, as Bordeaux are in third with seven points; two points shy of first-placed AS Roma with nine.
In another game, Roma eased off their Champions League worries with a deserved 3-1 win over FC Cluj in Romania.
Midfielder Matteo Brighi scored the opener for Luciano Spalletti's men on 23 minutes after being set up by Simone Perrotta.
In the 23rd minute, skipper Francesco Totti added the second from a delightful free from the edge of the box, before Youssef Kone hit Cluj's only goal of the game seven minutes later.
In the second half, Brighi put the result beyond doubt with a 64th minute goal.
Roma secure the group's top spot while Cluj remain fourth with four points.