The Air Seychelles flight carrying 128 passengers was forced to land on Monday because of an electrical malfunction.
Israel's Foreign Ministry said the passengers spent the night at an airport hotel in Jeddah and were flown back by the airline on an alternate plane.
Tracking data from FlightRadar24.com showed the Air Seychelles Airbus A320, flight HM22, diverted to Jeddah on Monday night while it was over the Red Sea.
The airline did not respond to a request for comment.
Another Air Seychelles A320 flew to Jeddah on Tuesday from Dubai to pick up the travellers and carry them on to Tel Aviv.
In 2022, Saudi Arabia lifted its ban on Israeli overflights during a visit by US President Joe Biden to the kingdom.
The passengers streamed out of Israel's Ben Gurion International Airport later on Tuesday, some seemingly surprised by the swarm of reporters, photographers and party balloons that greeted them.
Israel and Saudi Arabia do not have official ties, although they have developed strong but informal connections over recent years over their shared concerns about Iran's growing influence in the region.
After Israel and four Arab states signed normalisation deals in 2020 under the former US administration, Biden has been working to strike a similar agreement with Saudi Arabia.
Israeli Prime Minister Benjamin Netanyahu, who has made an agreement with Saudi Arabia a major goal, seized on the incident to highlight the potential for improved ties.
"I greatly appreciate the warm attitude of the Saudi authorities to the Israeli passengers whose flight was in distress," he said in a video recorded in Hebrew with Arabic subtitles, as he gestured toward a map of the region behind him.
"I greatly appreciate the good neighbourliness."
In interviews with Israeli media, the passengers said their experience in Jeddah was pleasant, with some Saudis even greeting them in Hebrew.
There was no immediate reaction in Saudi Arabia.
A normalisation deal with Saudi Arabia has the potential to reshape the region and boost Israel's standing in historic ways.
But brokering such a deal is a heavy lift as the kingdom has said it will not officially recognise Israel before a resolution to the decades-long Israeli-Palestinian conflict.
Saudi officials are also apparently seeking defence guarantees and access to US nuclear technology.
