The famed broadcaster also faced fresh pressure after reports that its chief executive George Entwistle, who quit dramatically would receive a staggering payoff of 450,000 pounds, which Prime Minister David Cameron said was "hard to justify".
BBC's director of news Helen Boaden and her deputy Steve Mitchell were asked to stand aside till an inquiry committee into Savile affair was completed, the broadcaster said.
The suspension of two executives follows resignation of the company's director general, leaving the broadcaster in chaos as it fights the fallout from allegations that its late star Savile was a serial sex offender and from a television report that wrongly implicated a Tory politician in child abuse.
Reports said that pressure was also mounting on BBC's chairman Chris Patten to quit as well as speculation that a number of senior figures at the BBC were set lose their jobs.
The chain of resignations follows a report into a Newsnight broadcast on abuse claims, which said the BBC must resolve a "lack of clarity" in the chain of command.
The quiting of the director general with a fancy pay-off triggered off widespread protests, with the Prime Minister saying it was a matter for George Entwistle's conscience as to whether he expected the full payoff - a year's salary after just two months in the job.
Culture secretary Maria Miller said: "The [BBC] Trust will need to justify this - it is accountable to licence fee payers in ensuring value for money, and we expect it to have considered that carefully."
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The opposition Labour party asked for an urgent question in the House of Commons on the pay-out.
Reports said that the two executives had removed themselves from making decisions on some areas of BBC News output while a separate inquiry, by former head of Sky News Nick Pollard, was held into that decision.
Ken MacQuarrie, director of BBC Scotland, in his report on the north Wales broadcast, said: "To address the lack of clarity around the editorial chain of command, a decision has been taken to re-establish a single management to deal with all output, Savile-related or otherwise.
"Helen Boaden has decided that she is not in a position to undertake this responsibility until the Pollard review has concluded."
He added: "Consideration is now being given to the extent to which individuals should be asked to account further for their actions and if appropriate, disciplinary action will be taken."
The BBC said once the Pollard Review reports, Ms Boaden and Mr Mitchell "expect to then return to their positions".