Sergio Rico featured ahead of Keylor Navas in PSG's goal with Timothee Pembele, Presnel Kimpembe, Marco Verrati, Rafinha and Moise Kean the other changes from the win over RB Leipzig.
A stroke of good fortune from the host gave Bordeaux the lead in the first ten minutes as persistent pressure from Maja forced Pembele to find his own net from a corner-kick.
Alessandro Florenzi were metres away from bringing PSG level three minutes later from a low shot on the right following a darting move, but Bordeaux goalkeeper Benoit Costil came up trumps.
PSG cancelled out the visitors' opener when Neymar Junior stepped forward from the penalty spot to send Costil the wrong way from a foul in the box.
It became more for the all-conquering Ligue 1 champions 28 minutes in as Kean made the most off a loose ball from Costil following a shot by Neymar to convert with ease.
Kylian Mbappe, who netted a double in a 3-2 loss to Monaco last Friday, came close to a third for the home side six minutes later but watched his tipped onto the frame of the goal by Costil.
Bordeaux went to the substitutes bench at the start of the second half and introduced Loris Benito for Enock Kwateng, as PSG stayed unchanged from the first half.
The move worked midway through the second half after Yacine Adli exchanged passes with Hatem Ben Arfa before curling beyond the reach of Rico.
Both sides launched numerous attacks for the winner late on, as Neymar struck the roof of the net before Rico pulled a superb block to deny Nicolas de Priville, leaving the spoils shared.