Trossard experienced discomfort in his left leg and was substituted before half-time, with manager Mikel Arteta confirming they did not want to take any risks.
The injury is a significant blow for Arsenal, as Trossard has been their most productive attacking player this season, contributing five goals and five assists.
Noni Madueke replaced Trossard and scored Arsenal's second goal, while Gabriel Martinelli and captain Martin Odegaard also returned from injury during the match.
Mikel Arteta is expected to provide a further update on Trossard's condition and the status of other injured players ahead of the Chelsea fixture.