The reverse-swing specialist suffered a twinge in his left knee during Glamorgan's C and G Trophy match against Ireland on Monday and saw a specialist Thursday to get further information on the problem which forced him home from the tour to India.
Now Jones has been advised to rest for six weeks, which rules him out of the Test and one-day series against Sri Lanka, and he could face further surgery at the end of it.
Dr Peter Gregory, the England and Wales Cricket Board's chief medical officer, said Friday: "Simon had an MRI scan, and his injury was reviewed by his orthopaedic specialist yesterday.
"The view of this specialist is that Simon sustained a new injury to his knee, which has damaged the cartilage surface of the joint.
"Simon will be required to rest the knee for six weeks and will then be reassessed. If the knee does not respond to rest he may need to undergo further surgery."
It was desperate news for Jones, the son of former England left-arm quick Jeff. He endured a 10-month battle to play again after suffering torn cruciate ligaments in his right knee during the 2002-3 Ashes tour of Australia.
He recovered to become a key member of last year's Ashes triumph but has not played a Test for England since the thrilling victory at Trent Bridge in August.
Jones's latest setback saw him become the latest England player to be ruled out as the selectors prepare to announce their squad on Sunday.
The Welshman's fellow quick James Anderson (stress fracture of the back) has been ruled out for anything up to two months while spearhead paceman Stephen Harmison's shin problem has means the Durham fast bowler will not take the field when the first Test starts at Lord's on Thursday.
England had long been resigned to being without captain Michael Vaughan as the Yorkshire batsman deals with the latest effects of a longstanding knee problem while left-arm spinner Ashley Giles has yet to make his comeback after operations for hip and hernia injuries.