Les Phoceens found themselves trailing at home with around 11 minutes remaining before Jordan Ayek and Andre-Pierre Gignac snatched all three points.
The result keeps Marseille hot on the heels of Ligue 1 leaders Paris Saint-Germain, who play at Bordeaux tonight.
"You have to persevere in football, always believe right up to the last minute," said Baup.
"It's true there was a moment when we came close to going 3-1 down, but there is a squad dynamic in football, and we've shown that this season. We're capable of turning situations round.
"Whether it be at Sochaux or against Montpellier, it's clear we have to improve our use of the ball at the back. But with our attitude, that unity, that desire to shake things up, we can hope to pick up more points and continue to trouble bigger teams."
Marseille make the trip to face Rennes next Saturday.