The Denmark striker scored his fifth goal of the season with a deflected shot that looped over Lyon keeper Remy Vercoutre with just eight minutes remaining.
Braithwaite's effort cancelled out Alexandre Lacazette's first-half opener and gave Toulouse their first point in Lyon since 2006.
With the points shared, the two sides remain level on points, with Lyon ahead in 12th place by virtue of a better goal difference.
Toulouse sit in 14th, with Lorient also on 20 points and lying between the two.
All three teams are some way off the pace set by league leaders Paris Saint-Germain, who have 37 points.