Shoaibi scored the winning goal five minutes before the end of regular time. Zakaria Abu Khalal had opened the scoring for Toulouse, but Alexei Bosetti equalized from the penalty spot.
With this, Toulouse qualifies for the tournament final for the first time, after losing in the semi-finals on five previous occasions.
In the final, which will be held on April 29, Toulouse will face defending champions Nantes, who beat Olympique Lyonnais 1-0 on Wednesday..
Abu Khallal opened the scoring in the 36th minute with a header, but Anisi equalized in stoppage time in the first half from a penalty kick that Bosetti got after he was fouled inside the penalty area..
But Chaibi dashed the hopes of the Annecy fans to repeat the achievement of the quarter-finals, when he beat Olympique de Marseille, in the 85th minute, as he scored from close range after a fatal defensive error by Arnold Thimonfo.
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