The hosts led at half-time thanks to goals from in-form Dimitri Payet and Turkey winger Cengiz Under before 18-year-old defender Timothee Pembele and substitute Remi Oudin, with a well-worked volley from a corner, scored for the visitors.
"Looking at the game at half-time, we were down 2-0. Then we get the draw. Here, in Marseille, it's a good point," Oudin told broadcaster Prime Video. "It's the little details that mean you win or get a draw, like tonight. It's important," he added.
Home coach Jorge Sampaoli kept faith in the 11 which started last weekend's 3-2 win at Montpellier. The visitors' Yacine Adli was named on Vladimir Petkovic's bench due to the 21-year-old attacking midfielder's expected move to AC Milan.
There was a worrying sight after six minutes as Bordeaux's Samuel Kalu collapsed outside the home penalty box without any contact with an opposition player. Less than 90 seconds later Nigeria winger Kalu was back on his feet after treatment, he played on for five minutes before being substituted by Remi Oudin.
Under claimed his second goal in as many games after the half hour mark after Brazilian midfielder Gerson's cut-back. Payet added his third of the campaign four minutes before the interval with a sublime effort which started near the half-way line and finished with his low shot into bottom corner.
Petkovic's men were on level terms by the hour mark after Timothee Pembele, who joined on-loan from Paris Saint-German last week, and first-half replacement Oudin scored to claim the point before Leo Balerdi was sent off after 89 minutes for the hosts.