The NFL released a statement Wednesday saying that the matter was resolved but didn't provide details of the financial settlement.
"After a hearing with the Commissioner and the Finance Committee, the matter of the reimbursement of legal fees has been resolved to the satisfaction of all parties," the NFL said.
Jones had an appeal hearing with commissioner Roger Goodell on Monday in West Palm Beach, Florida.
The NFL sought the reimbursement of the legal fees that were incurred in Ezekiel Elliott's fight of a six-game suspension and in the threat of a lawsuit to block Goodell's contract extension.
In 1997, Resolution FC-6 was added to the NFL's constitution, giving the commissioner power to seek reimbursement of fees if a team "initiates, joins, has a direct, football-related financial interest in, or offers substance assistance to any lawsuit or other legal, regulatory or administrative proceeding against the league."
ESPN's Todd Archer contributed to this report.