Jones has a torn ligament beneath his left big toe, sustained two weeks ago while doing rehabilitation on the left hamstring he hurt Oct. 12. The hamstring is healed, but he will need surgery on the toe and up to six months to fully recover.
"Obviously disappointed, certainly for him and us," coach Wade Phillips said. "But long term, he's going to be all right."
Until Thursday, when announcing that Jones will be placed on injured reserve, the Cowboys had not reported the toe injury. The practice report released by the team Wednesday, after Jones had limited participation, listed only the hamstring.
The Cowboys now say Jones, one of the team's two first-round draft picks, practiced then so they could evaluate his ability to play with the toe injury.
Team spokesman Rich Dalrymple said in a statement that Jones' participation in practice "was designated as a day to obtain a thorough evaluation on his current condition and his ability to perform all of the running tasks involved in playing in a game."
That was the first time Jones had practiced since hurting his hamstring.
Based on that practice session and an evaluation by Dr. Robert Anderson, a North Carolina-based foot and ankle specialist who reviewed an MRI of Jones' foot, the Cowboys decided Jones couldn't play again this season and that the best option for his long-term future was surgery.
Team owner Jerry Jones said the surgery would be done Saturday in Charlotte by Anderson.
Dalrymple said Felix Jones hurt his toe while doing some rehabilitation work Nov. 7, the Friday going into the team's open date. Phillips said Jones' toe bent back when his foot slipped while running on the grass.
In his six games, Jones rushed 30 times for 266 yards (8.9 yards per carry) with three touchdowns. The 22nd overall pick, the speedy Jones provided a change of pace to bruising Pro Bowl starting running back Marion Barber. Jones also returned 16 kickoffs for a 27.1-yard average, including a 98-yard touchdown.
"I think everybody saw what he did, not just the potential," Phillips said. "We think he's got a great future. That's why we want to make sure of that. It could be a problem if he doesn't get an operation fairly soon."
After Jones practiced Wednesday, Phillips revealed that "some other things came up during his injury rehab." But the coach wasn't specific then, other than to say it wasn't a knee injury.
The team owner did little later Wednesday to solve the mystery.
"There is more. What we are doing is evaluating that," Jerry Jones said. "There are parts of it we are having to look at intently and see if he has his strength in some areas, and some direction."
When asked for clarification then, the owner said, "We are trying to see if the `more' will allow him to play."
On Thursday, he got the negative answer.