The first direct commercial flight between Israel and Doha took off Sunday after Qatar approved the flights for World Cup ticket holders despite having no ties with Israel.
Football's world governing body FIFA said last week that Qatar had agreed to special direct flights, with Cyprus-based Tus Airways later confirmed as the approved carrier.
Israeli foreign ministry official Lior Haiat, at Ben Gurion airport near Tel Aviv, told AFP that "history has been made," with the "first direct flight from Tel Aviv to Doha."
When FIFA announced the deal for direct Israel-Qatar flights on November 10, it claimed that "Palestinian ticket holders and media" would be "able to travel on these chartered flights with no restrictions."
But it was not immediately clear to what extent Palestinian residents of the Israeli-occupied West Bank or blockaded Gaza Strip would have access to the charter.
FIFA said the arrangement would be subject "to Israel's security requirements."
Haiat repeated advice that Israelis behave prudently while in Qatar, a majority Arab nation that staunchly supports the Palestinian cause and does not recognise the Jewish state.
Hadar Segal, 35, told AFP that boarding the flight was a "special and historic thing."
He said he had plans to watch England play Israel's arch enemy Iran, as well as the match between Argentina and Saudi Arabia, another Arab country that does not recognise Israel.
Palestinian residents of the West Bank in most cases travel abroad from Jordan, with access to Ben Gurion airport heavily restricted.
Palestinians in Gaza do not have access to Israel or its airport, with very rare exceptions.
Qatar offers substantial financial support to Gaza and has served as an intermediary between Israel and Hamas Islamists who control the coastal enclave.
© Agence France-Presse