"I didn't think it was funny and neither did Zeke -- we actually thought it was disrespectful," agent Rocky Arceneaux told ESPN on Monday afternoon.
Arceneaux said Elliott continues his contract holdout while training in Cabo San Lucas "at a great facility."
Jones answered a question about Elliott after the Cowboys' preseason game Saturday in Hawaii with "Zeke who?"
The Cowboys owner then clarified he wanted Elliott to know he was just "cracking a joke at Zeke's expense."
Jones had been asked if running back Tony Pollard, who is having a strong training camp, was the best negotiating ploy the Cowboys have in talks with Elliott, which drew his response.
Arceneaux did not reveal any details related to contract negotiations.
Elliott has yet to report to training camp and is subject to fines totaling more than $900,000 as he seeks a contract extension.
Pollard had 51 yards on the Cowboys' first drive Saturday, which ended with his 14-yard touchdown run.
"He knows exactly what to do, and he knows how to do it, so it is, he goes out there and he plays to that level," Jones said. "If he continues this through the next several weeks, he's going to be right in the middle of it early, and that will really complement what we're doing with Zeke. Not replace that. And I mean that, not replace that. Nobody's getting cute here, but it'll certainly be a great complement. ... I can picture those guys same sets at the same times out there and really giving those defenses fits."
ESPN's Todd Archer contributed to this report.