About 16,700 spectators, including 2,000 Poles, saw the visiting team get on well with 2-0 lead for most of the time without Bayern Munich's striker Robert Lewandowski, who will undergo surgery in December.
Poland opened strongly and scored just after four minutes by Lokomotiv Moscow's midfielder Grzegorz Krychowiak, much thanks to an error in Israeli defense.
The Polish control of the game continued until halftime, when Israel was very lucky not to concede more goals.
Poland doubled its lead in the 54th minute by AC Milan's striker Krzysztof Piatek, who turned a rebound from the post to a second goal.
Guangzhou R&F striker Eran Zahavi, who shares with England's Harry Kane the lead of the qualifiers' top scorers table (11 goals each), found the net in the 75th minute, but the goal was disallowed because of the offside.
A late goal by Sevilla's striker, Munnas Dabbur, in the 88th minute, was not enough for Israel.
During injury time, an Israeli fan broke into the pitch, and security men who chased him accidentally hit two Polish players.
The Finnish referee Mattias Gestranius decided to stop the match, and only after pressure from Israel's players and staff he agreed to resume play.
With one match to go in the 6-team group G, Israel lost a chance to go directly to the final tournament, which will take place in 12 cities across Europe starting June 12, 2020.
However, Israel can still qualify for the finals through the playoff phase - thanks to the results it achieved in UEFA's Nations League tournament.
Poland secured its spot finals before the match in Israel, and will be joined by Austria, who defeated North Macedonia 2-1 on Saturday as well, and will finish second in the group.
The playoff draw will take place on November 22, and the games will take place on March 26 and March 31.