A bitter row about Mr Watson's position overshadowed the start of Labour's party conference in Brighton.
Labour's ruling National Executive Committee (NEC) had been expected to vote on a motion to abolish the post in a meeting on Saturday.
But following an intervention by party leader Jeremy Corbyn, the potentially explosive vote did not take place.
"This will consider how democratic accountability can be strengthened to give members a greater say, expanding the number of elected positions, and how diverse representation can be further improved.
"The NEC agreed to his proposal."
Mr Watson has publicly clashed with Mr Corbyn on a number of occasions and has been pushing for Labour to back staying in the European Union in any future referendum.
He recently called for a new Brexit referendum to be held before a general election.
Earlier on Saturday Mr Watson had said he was "taken by surprise" at the NEC move, telling the BBC that it had not been on the agenda.
Mr Watson said: "There was no warning.
"I got a text message in a Chinese restaurant in Manchester to say that they were abolishing me."
Mr Watson had told BBC Radio 4's Today programme: "What it shows is that this conference is supposed to be a platform for what could be a general election in six weeks.
"It's a straight sectarian attack on a broad church party.
"And it's moving us into a different kind of institution where pluralism isn't tolerated."
Former leader Ed Miliband said those responsible for trying to oust Mr Watson had "taken leave of their senses".
A surprise attempt to get rid of the deputy post on Friday failed at an NEC meeting - from which Mr Watson was absent - because it was ruled out of order.
Despite a 17-10 vote in favour of debating the motion - which was pushed by Jon Lansman of the Corbyn-supporting Momentum group - the necessary two-thirds majority to overturn a ruling of the chair was not met.
The attempt to remove Mr Watson provoked a furious response from Labour MPs at a time when the conference is meant to put Mr Corbyn's team firmly on an election footing.
Former Labour leader Mr Miliband had said: "The move to abolish the deputy leader post without warning or debate is undemocratic, wrong and should not happen.
"Those who came up with the idea for the eve of Labour conference have taken leave of their senses."
Ex-minister Yvette Cooper tweeted: "This is completely mad and incredibly destructive. Country faces serious challenges & General Election could be imminent. @UKLabour conference shd be about country & about pulling together. Instead we get this."
Former Cabinet minister Ben Bradshaw said the attempt to "purge" Mr Watson was "totally f****** insane".
Tottenham MP David Lammy said: "Tribal infighting in the middle of a Boris Johnson-inspired national emergency makes me want to weep.
"My constituents and millions of others across the country desperately need the Labour party united right now. The Tories, not Tom Watson, are our opponents. Let's fight them."