Coach Wade Phillips said Wednesday that Jones, who was injured early in the 20-13 loss at Pittsburgh, has a "herniated disk, maybe two" and will definitely miss Sunday's game against the New York Giants.
"Our people don't think it's career-threatening or anything else that he would have to be operated [on] or anything like that," Phillips said. "But it is something that might put him out this year."
However, NFL.com, citing a league source, reported Wednesday that the injury could threaten Jones' career.
Jones was scheduled to be evaluated by another doctor Thursday.
"The prognosis wasn't good for him playing this year, from our people," Phillips said. "They're going to see if maybe they can re-evaluate in a few weeks or they'll say you're not going to play this year. That's what we're looking at."
For the wild-card hopeful Cowboys (8-5), Jones added to an already lengthy injury list. Running back Marion Barber (right pinkie toe, calf), tight end Jason Witten (sprained right ankle), receiver Roy Williams (foot), safety Ken Hamlin (right foot) and guard Montrae Holland (ankle) were among those who did not practice Wednesday.
Jones was hurt in the first quarter Sunday when he fell on top of his muffed punt, getting caught in a scramble for the loose ball. After several players fell on him, Jones was pulled from the pile awkwardly by a Pittsburgh player. But Jones played the rest of the game.
It was Jones' first game back after a six-game suspension, the second time he has been banned by commissioner Roger Goodell for off-field issues.
Jones was not in the locker room Wednesday when it was open to reporters and not available for comment.
Phillips said he knew Jones was hurt when the coach was checking on players during the flight home.
"I ask them if they're OK, and he said, 'No, I'm not OK.' He said, 'No, my neck's hurting,'" Phillips said. "Most of them say, 'I'm OK, I'll be OK, Coach,' that kind of thing. But he obviously was hurt."
After starting the first six games for the Cowboys, Jones was suspended by Goodell on Oct. 14, a week after the cornerback got into an alcohol-related scuffle with one of his bodyguards during a private party at an upscale Dallas hotel.
The bodyguard was part of a security detail employed by the team to help keep the player out of trouble.
Goodell initially issued an indefinite suspension that he said would last at least four games. Jones was allowed to return to practice Nov. 24, but wasn't cleared to play until the Pittsburgh game.
Jones missed the entire 2007 season because of multiple incidents while with the Tennessee Titans, who traded him to Dallas during the offseason. Before playing last week, Jones had missed 22 of 28 games since the end of the 2006 season because of suspensions.
Jones had 28 tackles and a team-high 13 pass breakups in his seven games with the Cowboys.
"He did play some. I think that helped some," Phillips said. "We know a lot more about him as far as the player is concerned. It's up to him now. I told him he's being tested. He is."
When asked if Jones' attitude had been different since his return to the team after being away nearly six weeks because of the latest suspension, Phillips said that had never been an issue with the Cowboys.
"He practices and meets and does all the right things," Phillips said. "We've never had a problem with his on-the-field and practice attitude. He wanted to play and I thought he played pretty well in the game. He was just getting back."
Barber, who didn't make the trip last week to Pittsburgh, worked with trainers on the side Wednesday. Phillips said he would be re-evaluated Thursday to see "how he feels and where he is."
Information from The Associated Press was used in this report.