Punches and profanities were exchanged between the handful of youngsters, who waved Palestinian and Turkish flags throughout the match, and the Haifa players, who were mainly stunned by the scenes.
The security stewards on hand were slow to react, but ultimately the situation calmed down, with several of the protesters being escorted out of the stadium and the Haifa players leaving the pitch unscathed.
Lille was leading 2-0 when the match was stopped.
Haifa only finally made its way back to the hotel with a police escort after more than an hour, with some of the protesters waiting for the team outside the stadium.
"Maccabi Haifa Football Club believes in co-existence, tolerance and is against violence," a club statement read. "We denounce the violence that was used against us. This didn't happen because of sport or football, it happened because we are a team which represents Israel."