North Macedonia had won their previous six home games, scoring 19 goals.
Poland are on nine points, two ahead of Israel, in second place after Zahavi's superb performance earned them a comfortable victory in Latvia.
The top scorer of the qualifying phase curled in a fine free-kick after 10 minutes and added another on the hour.
He completed his second hat-trick in a row in the 81st to take his tally to seven goals in Israel's three qualifiers. Zahavi had also got three in a 4-2 win over Austria in March.
The Austrians earned their first points by beating Slovenia 1-0 thanks to Guido Burgstaller's 74th minute winner.
Burgstaller scored on the rebound after Marco Arnautovic's effort was saved.
Austria are fourth on three points, one ahead of the Slovenia and one behind third-placed North Macedonia.
(Reporting by Karolos Grohmann; Editing by Ken Ferris)
