The Frenchman turned in Grant Holt's cross 12 minutes from time to claim Wigan's first goal away from home in nine matches.
Prior to this game, Owen Coyle's men had last scored on their travels in a 4-0 win over Barnsley on the opening day of the Championship season.
Fortune saw two efforts cleared off the line prior to his goal, while Aston Villa loanee Marc Albrighton struck the crossbar for the visitors.
The win elevates Wigan to 10th place in the table, two points adrift of the top six with a game in hand.
Yeovil, meanwhile, have lost 10 of their 15 Championship games and remain rooted to the foot of the table, four points from safety.
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