Earlier Toulon continued their impressive home form with a 36-24 victory over Racing92 to consolidate third spot but lost skipper Charles Ollivon to an early injury.
A week after losing top spot to Toulouse, Bordeaux regained pole position while awaiting the French champions' trip to La Rochelle.
Yannick Bru's players took time to find their feet at Stade Français, with a slim 13-12 lead at half-time, but in a chilly capital managed to raise the temperature after the break with Louis Bielle-Biarrey touching down twice.
"It's a match where I'm happy to score two tries but not everything was good," said winger Bielle-Biarrey.
"We came here with a purpose, it's never easy to win here. Now we move on to the Champions Cup," he added of next week's trip to Exeter.
Toulon took the lead thanks to several brilliant moves from scrumhalf Baptiste Serin before being worried in the second half.
Gael Drean touched down twice to bring his tally to ten this season, to consolidate third place with 43 points.
The victory was however overshadowed by Ollivon's injury exit.
The 46-times capped France flanker picked up a right knee problem in the sixth minute in an action when Fijian winger Setariki Tuicuvu touched down the first of his two tries, and was helped off the pitch.
Tuicuvu got his second try just seven minutes later.
The 31-year-old Ollivon's injury comes a week before Toulon host Harlequins in the Champions Cup and four weeks before France's Six Nations opener against Wales on January 31.
'Feet on the ground'
For Toulon the six-try victory was their ninth Top 14 win and eighth in a row at home in all competitions to consolidate third place and boost confidence ahead of Harlequins.
"I was honestly a little afraid of this match because Racing92 is a team capable of doing incredible things," said Toulon rugby director Pierre Mignoni.
"Now we have to feed off this progress without being satisfied. It is important to stay on a positive dynamic because we can lose everything in January.
"We're ambitious. We're hosting Harlequins, so we have to win while keeping our feet on the ground."
Bayonne, who had been equal on points with Toulon before the weekend, fell 42-10 at Montpellier, paying for a first half where they trailed 22-0.
The Basques finished the game with 14 men after Esteban Capilla's red card.
Montpellier's fifth success in a row at home moves them into the top six.
In a bottom-of-the-table clash Lyon beat Perpignan 17-12.
