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The Ligue 1 visitor had looked destined for penalties heading into the final stages against its Ligue 2 host, before the substitute rode to the rescue.
A horrendous defensive misread by Annecy allowed him to head past goalkeeper Thomas Callens into an open net and send his side to a first final since 1957.
Toulouse had originally seized the lead in the first half through Zakaria Aboukhlal, with the winger's low header drifted home off a Branco van den Boomen cross.
But its opponent had equalised on the stroke of half-time through a penalty for Alexy Bosetti, after Gabriel Suazo was deemed to have fouled him inside the area.
The result means Philippe Montanier's side can look forward to a clash with defending champion Nantes at Stade de France next month.