He called the Argentinian decision a "victory" for sport.
Palestinian Football Association president Jibril Rajoub later said, "The Argentinian Football Association cancelled the agreement it signed with the Israelis because it reached the conclusion that this match is a political one". For more than a decade, they've led an worldwide campaign to boycott Israel as a means to pressure the Jewish state to change its policies toward the Palestinians.
A senior official at the Argentine Football Federation said the national team chose to call off the match with Israel after receiving threats from terror group Hamas.
Palestinians opposed the sold-out game, who claim the eastern part of the city as the capital of their future state.
She said the Argentinians had not objected to that and that Messi had wanted to visit holy sites in Jerusalem.
The BDS, which last month initiated a wider campaign to persuade Argentina to withdraw from the fixture, described the game as a "political tool" that Israel sought to use to "cover up attacks on Palestinians on and off the field".
The World Cup warmup match had been scheduled to take place on Saturday.
Speaking on Wednesday, Miri Regev said the match was called off in the wake of "threats by terror elements sent to Messi and his family and to other players". "The fact that Argentina fans and human rights activists around the world succeeded in thwarting it gives us a lot of hope".
"At the current time in which the USA president and Israeli officials are trying to take Jerusalem off the negotiating table, it is important to see that people power can produce results", she said.
Argentina will begin the tournament in Group D against Iceland on June 16.
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The friendly soccer match that was scheduled for Saturday night at the Teddy Stadium in Jerusalem between Argentina and Israel will not take place, the Israeli embassy in Argentina announced late Tuesday night.
Israeli officials reacted bitterly to the cancellation of the game.
It was a change of tone from Rajoub, who on Sunday had called for Palestinians to burn pictures of Messi and replicas of his shirt if he took the field in Jerusalem.
At the entrance to the news conference was a placard saying "From Palestine, thank you Messi" with Argentinian and Palestinian flags, under a big photo of Mr. Rajoub posing with the Barcelona ace.
Hamadeh Freij, a journalist in Gaza, said that people in the besieged territory were excited about the decision and that the issue dominated discussions during iftar.
Palestine Liberation Organization Secretary General Saeb Erekat gave thanks to "Argentina and its fearless people as well as its distinguished football team for choosing to abide by the principles of global law".
Claudio Tapia, president of the AFA, apologised for cancelling the match but said the safety of the players was at stake.
"It's nothing against the Israeli community, the Jewish community and I would like everyone to take this decision as a contribution to world peace", he said.
Jibril Rajoub, head of the Palestinian football association, had encouraged fans to burn shirts bearing Messi's name if he made a decision to play.