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.
PFA President Jibril Rajoub accused Israel of "politicizing sport" by hosting the match in Jerusalem.
The Albiceleste will not be playing their final World Cup warm-up game after the controversial match with Israel sparked protests.Argentina's controversial friendly against Israel has been suspended after threats towards Lionel Messi and waves of protests.
The famous Argentinian striker Gonzalo Higuain said that they had "finally done the right thing". Let us know in the comments section below.
The Argentine Football Association said they had informed their Israeli counterparts about the decision.
The Gaza clashes reached their peak on May 14, the eve of the 70th anniversary of the Nakba Day (the Day of Catastrophe), which coincided this year with the U.S. embassy relocation from Tel Aviv to Jerusalem al-Quds.
The Argentina Football Association did not immediately comment on the reports.
Marcos Rojo wants to feel like what it is to win a World Cup rather than the agony he experienced for Argentina when they lost to Germany 1-0 after extra-time in 2014, he said on Tuesday. "We are seeing it as crossing a red line and we can not accept it".
120 Palestinians were killed by Israeli forces in recent protests sparked by Donald Trump's decision to relocate the United States embassy in Israel from Tel Aviv to Jerusalem.
"From a sporting point of view, I would have preferred to play in Barcelona", Sampaoli said. Israel regards Jerusalem as its "eternal and undivided" capital.
At least 125 Palestinians have been killed there since 30 March.
Croatia and Iceland are their other two opponents in Group D and Rojo feels Argentina's progress in the tournament would depend on Lionel Messi's goalscoring abilities. Israel considers the entire city to be its capital, while the Palestinians seek east Jerusalem as the capital of a future state.
Jerusalem Affairs Minister and candidate for the upcoming Jerusalem mayoral election Ze'ev Elkin rejected claims that "politicization" of the exhibition soccer game with Argentina caused the cancellation.