The aircraft experienced technical difficulties while flying to Tel Aviv.
Photos showed the plane landing and passengers disembarking at Israel's Ben Gurion Airport in Lod, near Tel Aviv, after leaving Jeddah.
Israel's Foreign Ministry said the passengers had spent the night at an airport hotel in Jeddah and were flown back by the airline on another plane.
Israel and Saudi Arabia have no diplomatic ties.
In a short video statement, Mr Netanyahu praised Saudi Arabia for their "warm attitude".
"I greatly appreciate the warm attitude of the Saudi authorities to the Israeli passengers whose flight was in distress and was compelled to make an emergency landing in Jeddah," Mr Netanyahu said.
In July last year, Saudi Arabia opened its airspace to all countries, including Israel, coinciding with a visit by US President Joe Biden to the region.
Saudi authorities did not comment on the landing.