Les Violets had done all the hard work in Wednesday's first leg, racing into a three-goal lead to effectively kill off the tie ahead of this return fixture.
Substitute Jimmy Durmaz prevented the match from finishing goalless, popping up two minutes from time to ensure that Toulouse will once again compete in the French top flight for another year.
Toulouse looked more lively in the second half, with Max Gradel coming close on a couple of occasions, but they were struggling to open their account.
Durmaz powered the ball home after a corner came into the box, condemning Ajaccio to another season in the second tier.
TOULOUSE (4-3-3): Lafont; Amian, Diop, Jullien, Moubandje; Imbula (Blin 64'), Sangare, Toivonen (Durmaz 64'); Somalia (Jean 86'), Sanogo, Gradel
AJACCIO (4-4-1-1): Mandanda; Hergault, Sainati, Avinel, Cabit; Maazou (Pierre 79'), Vialla, Boe-Kane, Keita; Laci (Cavalli 60'); Nouri