The corporation has also overhauled the "chain of command" overseeing the BBC's journalistic output, in response to a botched Newsnight report.
The BBC has been in crisis as a result of a Newsnight programme which mistakenly implicated Lord McAlpine in a sex abuse scandal and the ongoing issues arising from revelations about Jimmy Savile's abuse.
Mr Entwistle quit on Saturday night over his handling of the growing problems, and there have been calls for Lord Patten, the chairman of the BBC Trust, to follow suit.
Ken MacQuarrie, the director of BBC Scotland, has delivered a report into the failed Newsnight investigation.
But the BBC said the temporary departures of Ms Boaden and Mr Mitchell from their roles were not as a result of the bungled Newsnight programme. Instead, they were in response to the "lack of clarity" surrounding who is in charge while the Pollard Review is making its inquiries.
This review - led by former Sky news chief Nick Pollard - is looking into an earlier decision to shelve a Newsnight investigation into Savile's sexual abuse.
The BBC said today: "The BBC wants to make it absolutely clear that neither Helen Boaden nor Stephen Mitchell had anything at all to do with the failed Newsnight investigation into Lord McAlpine.
"Whilst recognising this, the BBC also believes there is a lack of clarity in the lines of command and control in BBC News as a result of some of those caught up in the Pollard Review being unable to exercise their normal authority.
"In the circumstances, Helen and Stephen will be stepping aside from their normal roles until the Pollard Review reports and they expect to then return to their positions."
The BBC's head of newsgathering, Fran Unsworth, and Ceri Thomas, the editor of the Radio 4 Today programme, are to fill in for Ms Boaden and Mr Mitchell temporarily.
Karen O'Connor - a former deputy editor of Panorama and Newsnight - has also been drafted in as acting editor of Newsnight.
Findings of Mr MacQuarrie's investigation are expected to be made public later today. His report was one of the first things to be considered by acting director-general Tim Davie, who was appointed on Saturday and who is trying to rebuild trust in the corporation.
The BBC 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."
It went on: "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 Ms Boaden had decided that she was "not in a position to undertake" her role as director of news until the Pollard review had concluded.
Ms Boaden's position had been in question for several weeks, since the Savile scandal erupted early last month when it emerged she had a brief discussion with Mr Entwistle - then BBC director of vision - about a proposed Newsnight investigation into the late DJ's alleged abuse.
There have been repeated suggestions that the investigation was shelved because the BBC had planned tribute programmes to Savile, although the BBC has denied this.
Mr Davie last night held his first meeting with the BBC Trust since being drafted in as a stand-in for Mr Entwistle.
But his efforts to move on will be hampered by a row which has erupted over the disclosure that Mr Entwistle - who served just 54 days in the post - was to receive a full year's salary of £450,000 in lieu of notice.
Under the terms of his contract he was entitled to only six months' pay, but the Trust said the additional payment had been agreed as a reflection of his continuing involvement with the various BBC inquiries now under way.
The package was greeted with anger and disbelief by MPs. The chairman of the Commons Culture, Media and Sport Committee, John Whittingdale, said the Trust had to explain how it could justify such a large pay-off.
"A lot of people will be very surprised that somebody who was in the job for such a short period of time and then had to leave in these circumstances should be walking away with £450,000 of licence fee-payers' money," he said.
The future of Newsnight may also be in the balance, with Lord Patten warning there would have to be some "tough managerial decisions".
Lord Patten, however, acknowledged that the corporation needed to "get a grip" and turn the situation around or his own position would be on the line.
A BBC Trust spokesman said Mr Davie, who had only recently been appointed chief executive of the commercial arm BBC Worldwide, will be setting out his plans for dealing with the issues raised by the broadcast "as a first step in restoring public confidence".
Tory MP Philip Davies, a member of the Commons Culture, Media and Sport Select Committee, has called for Lord Patten to step down as BBC Trust chairman.
Asked for his reaction to the decision to pay Mr Entwistle a year's salary, he said: "I think it is absolutely astonishing, it is unacceptable, it is unjustifiable and it is an affront to licence fee-payers."
He continued: "Lord Patten is part of the problem. He is saying get a grip now because the whole issue is overwhelming him. But he wasn't saying that when he took over at the BBC, he seemed to treat it as some kind of sinecure post, that he could get a well-paid job and do very little.
"He has been asleep at the wheel. He wasn't saying that the BBC needs a radical overhaul when he took over or in the first year of him being in the job. Lord Patten's position is untenable, he has been a disaster as the chairman of the Trust."
Mr Davie told staff he was "determined to give the BBC the clarity and leadership it deserves", and said management would pull together as "one team".
He said he would continue the work begun by Mr Entwistle, to deliver "the best of British creativity", adding: "There will be no handbrake turn."
In an email to all BBC staff, he said: "The last few days and weeks have been exceptionally tough for the BBC.
"George's departure on Saturday night was a sad moment - for George and the whole BBC. His manner of leaving matched what we know about him: he is a good and honourable man who stepped down in the interests of the BBC."
He went on: "The BBC is a precious institution and I am determined to give the BBC the clarity and leadership it deserves in the next few weeks.
"What I will also do is continue what George set out - to work tirelessly on getting rid of anything that gets in the way of delivering the best of British creativity to our audiences.
"Following Ken MacQuarrie's initial findings into the Newsnight broadcast on 2 November, I believe there is a lack of clarity in the lines of editorial command and control in BBC News, with those caught up in the Pollard Review being unable to exercise their normal authority.
"So I have decided to ensure total clarity and re-establish a single management to deal with all News output, Savile-related or otherwise."
He reiterated that Ms Boaden and Mr Mitchell did not have anything to do with the failed Newsnight investigation on November 2.
Mr Davie said: "You can expect to see management pulling together as one team, focused on tackling the problems the BBC currently faces head on.
"But I also expect you to continue to make the programmes and services that our audiences love and that make the BBC unique."
