His concert had earlier been disrupted by fans dismayed at the booking, repeatedly heckling the performer and asking him to cancel.
Security was called and audience members threatened with removal.
A Facebook page was set up to urge the legendary perfomer against going ahead with his Israel appearance.
It stated “This is a huge mistake from an enduring cultural and political hero. Let’s see if we can change his mind.”
Over one thousand people have joined the page.
Scott-Heron is perhaps best-known for the classic The Revolution Will Not Be Televised, and was a leading voice in calling for the cultural boycott of apartheid South Africa, joining United Artist Against Apartheid in the 1980s.
His sharply political songs have provided a space for his own militant, anti-racist politics.
With Palestinian artists and musicians calling for a cultural boycott of Israel, campaigners were deeply saddened by Scott-Heron’s apparent decision to play a high-profile gig there.
“Gil Scott-Heron’s music has always been about fighting racism,” said protestor Sara el-Sheekh.
“But Palestinians daily face the most terrible oppression from the Israeli occupation – easily comparable to apartheid in South Africa.
Musicians and artists should not be giving this apartheid state any legitimacy.”
It’s great news that this date has been cancelled. Scott-Heron was cheered and applauded when he made his announcement.”
Campaigners have vowed to continue the fight for a cultural boycott of Israel.