The former Asante Kotoko ace was substituted in the 31st minute by Ben Romdhane.
Bonsu is set to undergo scans in the coming days to reveal the extent of injury and how long he could be out of action.
The 25-year-old has been one of the consistent players for the Red and Golds since joining them last summer from Ghana Premier League giants Asante Kotoko.
Esperance dominated the game but failed to hit the back of net at the Stade Olympique de Rades.
Esperance lead their group with seven points after three games played so far, just a point above Moroccan side Raja Casablanca.
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