The 32-year-old Vaughan, who led England to their Ashes win in 2005, has not played international cricket for over a year because of a knee injury and underwent surgery to cure the problem.
His first match back at the helm will be Tuesday's international Twenty20 match in Sydney.
The tourists then face Australia and New Zealand in a triangular one-day series which begins against the Australians on January 12.
"It will be a fantastic boost to have Michael Vaughan back as captain for the one-day series," said England's chairman of selectors David Graveney.
"His leadership experience will be invaluable as we prepare for a tough series against an excellent Australian team.
"It is to Andrew Flintoff's credit that he was prepared to take on the responsibility of leading the Test side in Australia in Michael's absence.
"But Michael is the England captain and he will now begin the task of preparing the team for the challenges that lie ahead this winter."
Vaughan, who has a meagre One-day average of 28.36 from 74 appearances, will be expected to stay in charge for the World Cup in March and April, if he comes through the series here unscathed.