It was the home side who started the stronger, and had the ball in the net early after a well-worked move, but it was ruled offside by the referee.
Toulouse went back on the attack and thought they had taken the lead, but Raphael Guerreiro was able to clear a shot off the line.
The hosts then had the closest chance of the half, when Yann Jouffre struck the post with a free kick just minutes before the break.
Toulouse hit the frame of the goal once more shortly after half time, when Braithwaite couldn't quite direct his diving header on target.
However, the home side finally took the lead when Braithwaite pulled off a fabulous first touch before guiding his shot into the back of the net 19 minutes from time.
Toulouse move to 11th following the victory, while Lorient slip to 16th in Ligue 1.