Vaughan, 31, was ruled out of Wednesday's opening Test against the Indians with a recurrence of a right knee injury and returned to the United Kingdom until further notice.
The news was the latest in a catalogue of calamity for the tourists, who lost vice-captain Marcus Trescothick at the weekend for an indefinite period due to personal reasons.
Andrew Flintoff will now captain his country for the first time in an international, leading a side woefully short of experience having been shorn of its two most senior players.
Prior to this trip first-choice spinner Ashley Giles pulled out due to a hip injury and fast bowler Jones is now the most serious of doubts after twisting his left knee in the nets today.
Welshman Jones had been expected to take the fourth fast bowling berth in the side on Wednesday, as long as he proved his fitness following a six-month lay-off due to ankle surgery. Now he is facing a scan on his injured knee.
Who now will line up in Flintoff's first match in charge is a matter of debate, with the back-up fast bowlers Liam Plunkett and James Anderson risks for differing reasons.
Plunkett has a bruised left heel, which is still causing a concern, while Anderson only arrived in India last night after being summoned from the England A tour of the Caribbean.
His partner on that 48-hour worldwide dash, Essex opener Alastair Cook, is now favourite to form a new first-wicket alliance with Andrew Strauss.
England's other option at the top of the order is Matt Prior, Geraint Jones' understudy as wicketkeeper.
Vaughan's latest setback continues a worrying trend which has developed over the last three years.
He had his right knee cleaned up in an operation prior to the 2002-03 Ashes campaign and underwent surgery again in December in a bid to be fit for this nine-week tour.
The problem flared ahead of the first Test in Pakistan, forcing him to sit out, and he missed the one-day series later on that tour to undergo surgery.
Although the England management have not ruled him out of the entire tour here, with the three-match series being a back-to-back format and a seven-match one-day campaign following a week later there is little time for him to regain match fitness.Reuse content