It has been claimed that "threats and provocations" had been made against the Blaugrana star, with some supporters even asking fans to burn Messi shirts if he did take part.
Opposition figures, however, accused Israel's headline-seeking sports minister of bringing on the politicisation of the sporting event by insisting on moving the game from Haifa to contested Jerusalem and by trying to orchestrate a photo-op with Messi. Let us know in the comments section below.
"It's a shame that Argentina's footballing nobility did not withstand the pressure from Israeli-hating inciters", he wrote on Twitter in the first response from an Israeli cabinet minister.
Obeid had urged Messi and his national team "to stand in solidarity with Palestinians and to boycott the scheduled game with Israel, which is occupying our land".
Tapia said, "The last 72 hours led us to make the decision not to travel", stressing that his primary responsibility was to look out for the health and safety of the team.
Neither the Argentine nor Israeli football associations have issued an official statement.
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Argentine media also reported the cancellation. "[Lionel] Messi can not turn his back on the Palestinian victims", said Jabareen, according to an Israel National News report.
Reports had surfaced in Argentina on Tuesday that the match would be called off, with Palestine's Football Association celebrating the news.
Israel considers all of Jerusalem its capital, while Palestinians want its eastern part as capital of their own state.
More than 115 Palestinians have been killed and almost 3,700 wounded during near-weekly protests along the Israeli border, according to Palestinian health officials. Israel regards Jerusalem as its "eternal and undivided" capital.
The cancellation came hours after pro-Palestinian activists staged a demonstration in front of the sports complex in Barcelona where Argentina are preparing ahead of the World Cup.
Palestinians and their sympathizers lauded Argentina's team for becoming the latest in a series of cultural figures to reconsider visits to Israel on political grounds.