Both Israel and Palestine claim the disputed city of Jerusalem as their capital, and the decision to stage the match at Teddy Stadium has prompted anger among officials at the PFA.
Israel have only previously played three senior international matches at the stadium, and played their most recent qualifier - a 3-0 defeat to Wales - in Haifa.
In a statement addressed to UEFA, the PFA said it was "resentful" of the decision.
Israel, who sit second in Group B, are also scheduled to face Cyprus in Jerusalem in October.
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