The PSG superstar gave his side the lead with his 30th league goal, despite a long VAR review, but was substituted early in the second half at Matmut Atlantique.
Jimmy Briand hit his sixth goal against the reigning champions to level the scores before Kylian Mbappe restored the lead, the France forward requiring treatment for cramp immediately after beating Benoit Costil.
Thomas Tuchel had overseen 14 wins out of 14 but Andreas Cornelius came off the bench to head home Maxime Poundje's cross to salvage a point for Bordeaux.
Bordeaux had the better early efforts with Briand having a header saved and Francois Kamano wasting two clear openings, but PSG took the lead in the 34th minute with a goal that was eventually awarded after the use of video technology.
Neymar started the move in midfield and arrived in the box to cushion in a first-time finish from Dani Alves' cross, though a check was required to see if Mbappe was in an offside position in front of goalkeeper Costil.
VAR was not needed to chalk off a potential second for Neymar, who had clearly strayed offside, while Angel Di Maria hit the post shortly before the break, with the Argentina attacker also denied by the woodwork in the second half.
Bordeaux again started the second half on top and drew level through Briand's excellent finish, the forward beating Alphonse Areola at his near post with a fine first-time strike.
Neymar limped off soon after and parity lasted just 13 minutes as Mbappe timed a run on to Julian Draxler's throughball perfectly to thump a shot beyond Costil.
Mbappe required treatment for cramp in the aftermath of his goal as PSG feared losing both of their superstar forwards, but the France international was able to continue.
And Bordeaux snatched a draw with six minutes to go, substitute Cornelius rising above a static PSG defence to direct a header that went through Areola's hands to ending the visiting side's historic run.
What does it mean? Cavani benched as run ends
Despite losing Neymar to injury, Tuchel did not turn to Edinson Cavani, who was named on the bench. Eric Maxim Choupo-Moting came on for the Brazilian instead as PSG's record-breaking run was halted, albeit they are still 14 points clear of Montpellier with another domestic title looking a formality.
Mbappe shoulders PSG burden
With Cavani sitting the game out and Neymar having limped down the tunnel, the pressure was on Mbappe to deliver. The PSG forward struck his 12th goal of the season - more than anyone in Europe's top-five leagues - and he was unfortunate it did not prove to be the winner.
Areola place under threat
Tuchel has delicately balanced the ongoing battle for the gloves between Areola and veteran Gianluigi Buffon, who arrived from Juventus on a free transfer to add experience. Buffon was left out but Areola's error for Bordeaux's leveller could see the 40-year-old finally become the club's undisputed number one between the posts.