James Hook (Ospreys) moves from inside centre to fly half and the Dragons' Ceri Sweeney fills the berth vacated by Thomas on the bench, covering a number of positions in the back line.
"Stephen has been nothing short of inspirational in camp over the last few days and this is by no means ideal preparation for what is an important week for us all," said Wales Coach Gareth Jenkins. "However, we are all confident James Hook will be able to change position and meet the challenge presented to him and Alfie's (Thomas) inclusion has positive implications both psychologically and for rugby reasons.
"We are in the privileged position of being able to call upon a player of his immense captaincy pedigree, rugby history and leadership talents to fill the void left by Stephen's injury. Alfie has captained Wales to a Grand Slam and led the British & Irish Lions as well as earning 91 caps in a career that has seen almost everything rugby has to offer.
"He will equal Gareth Llewellyn's 92 cap record on Saturday as most capped man in Senior Welsh rugby and it's fantastic for us to be able to fall back on someone of his stature and respect in the game. It is a credit to him that he responded so positively to his country's call when asked to do the job.
"This is an important weekend for Welsh rugby and Alfie has the capacity to come into the captaincy role and lift everyone. He was the natural candidate to fill in as captain for this game once we realised Stephen was not going to make it."
Jones suffered an impact injury to his hand; in addition to the well documented eye injury, during the Italy match which was under observation by medical staff, but improved sufficiently to allow him to be passed fit for selection. However, the injury was aggravated during a training session on Tuesday morning and further investigation revealed a fracture.
"Stephen didn't recall sustaining the impact related injury during the Italy game, but it was noted and monitored at that time," added Wales Team Physiotherapist Mark Davies.
"The wrist improved, along with his eye injury, and he was made available for selection before further aggravating the problem in training. A scan has revealed an uncommon injury in the form of a break to a small bone in his right wrist, which limits his ability to function.
"As a result the wrist will be put in a splint and immobilised for the next two to three weeks. The problem doesn't require surgical intervention."