He will undergo scans in the next few days to discover the full extent of the problem.
But Toulouse are already expect to be without the France international for the next three weeks.
It is a major blow for the defending European champions who have already been without former All Black scrum-half Byron Kelleher for almost three months.
Team-mate Clement Poitrenaud said: "It's a big disappointment for Freddie and for the team. He is a big player for us, especially for an important game like the quarter-finals of the Heineken Cup."
The injury marred what was otherwise a moral-boosting victory for Toulouse on the eve of their quarter-final against Biarritz Olympique next weekend.
Tries in either half by captain Jean Bouilhou and Yannick Nyanga saw Toulouse claim only their second victory in 11 years at Stade Aime Grial.
The result was also a bitter disappointment for Perpignan, who led 21-14 through tries by Guilhem Guirado and Adrien Plante before Jerome Porical, who kicked 14 points, saw his last-minute penalty sail wide of the posts.
Perpignan are also sweating on the fitness of centre Farid Sid ahead of their Heineken Cup quarter-final against Toulon.
Sid limped off after just five minutes with a knee injury.