Vaughan suffered the injury during his team's drought-breaking win over New Zealand in the triangular One-day series at Hobart's Bellerive Oval on Tuesday and it was initially assessed as a grade one tear to his left hamstring here Wednesday.
The injury was to be assessed over the following 48 hours, but Vaughan was travelling to Brisbane with the rest of the England squad.
Although it is believed it is only a slight tear, he will definitely miss Friday's clash with Australia in Brisbane and is also in doubt for the following two clashes in Adelaide, against New Zealand on January 23 and Australia three days later.
Lancashire batsman Mal Loye has been called into the England squad.
Vaughan's absence also means England will again have to assess their options for the captaincy, with Andrew Flintoff and Andrew Strauss the two contenders.
Flintoff was at the helm as England lost the Ashes 5-0, but has looked a much better player since handing over the reins to Vaughan for the one-dayers, culminating in his man-of-the-match performance against New Zealand.
Strauss has had an indifferent tour, several times falling to poor umpiring decisions, but his appointment as captain would keep the pressure off Flintoff.
Vaughan's injury occurred in only his second game back from an absence of over a year due to knee surgery.
He suffered the injury in the field against the Kiwis and although he still opened the England innings, he eventually had to call on Jamie Dalrymple to act as a runner.
Vaughan's injury comes on top of the rib injury sustained by star batsman Kevin Pietersen, who has returned to England but flagged the possibility that he may return if his side reaches the triangular series finals.