© UnknownA group of about 20 people had gathered outside the hall to protest the appearance of the orchestra
The soloist, Gil Shaham, was about to play Bruch's violin concerto conducted by Zubin Mehta when some people in the audience began booing and shouting.
BBC Radio 3 interrupted its live broadcast twice before returning later.
The Palestine Solidarity Campaign had earlier called on people to boycott the concert and urged the BBC to cancel it.
The pro-Palestinian group claimed that the IPO showed "complicity in whitewashing Israel's persistent violations of international law and human rights".
The BBC Proms Team tweeted: "We're sorry that the concert was taken off air following hall disturbance. Glad both pieces were heard by the audience in the RAH."
It later added: "We regret that as a result of sustained audience disturbance tonight's concert was taken off BBC Radio 3."
The performance was interrupted at about 19:45 BST and coverage was cut off again an hour later after more protests.
Outside the concert hall a group of about 20 campaigners waved banners and sang songs in protest against the appearance of the Israel Philharmonic Orchestra (IPO).
There were increased security measures including bag searches and a heightened police presence.
Police said there had been no arrests but there were heated exchanges between not only supporters of both political sides but concert-goers angry at the disruption to their evening.
Unless the protesters came equipped with ear plugs, it's a safe bet this might have been staged to garner sympathy for the poor suffering-never-ends psychotic cult of isis' ra' el.