Despite appealing to Goodell for leniency, Jones will have to pay a significant portion of the league's legal fees, which paid for lawyers to defend six owners that Jones had threatened to sue.
Jones must pay the league about $2 million, according to three people with direct knowledge of the decision who were not authorized to speak publicly about it.
The NFL chose to go after Jones and his pocket to also exercise a resolution made way back in 1997 which states that any owner who takes part in a litigation process involving other owners should later reimburse them for all the legal expenses made.
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"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 National Football League said.
The latest battle between Roger Goodell and Dallas Cowboys owner Jerry Jones is over, with Goodell coming out on top. Rather, it was really just a reimbursement of legal fees that Jones cost the league.
Cowboys owner Jones meanwhile retaliated by seeking to delay confirmation of a new five-year contract for Goodell, which had been previously agreed by the league's compensation committee.
After eventually relenting, Jones said after the owners meetings in December that he got what he wanted with an agreement to consider changes to the power of the commissioner's role through the league's constitution.