Fans threw bottles onto the pitch and some entered the field of play, causing the match to be ended early.
Al-Faisaly’s Twitter account said “our team left the stadium to go to our residence in preparation for departure… to Amman”.
Two Palestinians clubs, Hilal Al-Quds and Jabal Al-Mukaber, were due to play later on Tuesday, while the final match is scheduled for Friday.
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The friendly tournament was held for the first time in March last year with four Palestinian teams participating alongside the same two Jordanian teams. Al-Wehdat eventually won the title.
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The tournament is organised by the Palestine Football Association (PFA) and the opening match was played with PFA head Jibril Rajoub in the stands.