The Saints, along with general manager Mickey Loomis, head coach Sean Payton and assistant coach Joe Vitt, were notified that after careful consideration Goodell had upheld the measures imposed for continuing violations of the league's anti-bounty rule that endangered player safety over a three-year period.
Following a lengthy investigation, the league last month fined the Saints $500,000 and two second-round draft picks and suspended Payton for one year, Loomis for eight games and Vitt for six games.
Former Saints defensive coordinator Gregg Williams, who was at the heart of the pay-for-pain system, did not appeal his indefinite suspension.
Goodell said in a statement the club and the individuals would be expected to cooperate in any further proceedings and to assist in the development and implementation of programs to instruct players and coaches at all levels on principles of player safety, fair play, and sportsmanship.
The commissioner added he would consider mitigating the financial penalties on the individuals if they embraced the opportunity and participated in the programs in a constructive way.
Goodell said he would also consider whether there are factors that would support modifying the forfeiture of the team's 2013 second-round draft choice.
At the conclusion of their suspensions, the commissioner will review the status of each of the three individuals to determine their eligibility for reinstatement.
A three-year investigation by the league found that Saints defensive players received cash payments for a program that included "bounty" payments for "cart-offs" and "knockouts" -- plays on which the opposing players were forced to leave the game.