An NFL investigation found that, under Payton's watch, an assistant ran a program offering cash payouts for hits that knocked targeted opponents out of games or hurt them so badly they needed help getting to the sideline.
Given recent history, at least some of those penalties are likely to be tough, too.
The Saints case represents perhaps the starkest example yet of the sea change that the NFL has undergone since medical research and media reports on the long-term damage suffered by football players through concussions began to gain attention.
As recently as October 2009, while testifying before Congress, Goodell did not acknowledge a link between head injuries on the field and brain diseases later in life. And hundreds of NFL retirees are now suing the league for health problems they say began with their playing careers.
Yet the league has taken a series of steps to better protect players in the past couple of years, and just last month expanded the definition of "defenseless players" who may not be hit in the head or neck and cannot be hit by someone leading with a helmet.
While NFL veterans say off-the-books incentives have been around for years, and some current players claim tough talk about hitting opponents where they are injured happens in locker rooms throughout the league, Goodell responded to the Saints case by handing out unprecedented penalties.
In addition to upholding Payton's suspension, which begins next Monday and runs through the Super Bowl in February 2013 - by coincidence, in New Orleans - Goodell also affirmed suspensions of eight games for Saints general manager Mickey Loomis and six games for assistant head coach Joe Vitt. He also kept in place a $500,000 fine for the franchise and the loss of draft picks this year and next.
Loomis, who along with the team declined comment Monday, and Vitt begin their suspensions after the preseason ends.
Suspensions for New Orleans players who participated in the bounty pool could be coming within days.
The NFL has said as many as 27 players also could be sanctioned in the scandal. That might include former Saints defensive regulars who have signed elsewhere.
The league's investigation found that Williams' bounty system, which ran from 2009 through 2011, offered cash payments of $1,500 for "knockouts," in which an opposing player was knocked out of a game, or $1,000 for "cart-offs," in which an opponent needed help off the field. The league has said the bounty pool grew as large as $50,000.
The investigation also found that Payton initially lied about the existence of a bounty program and instructed his defensive assistants to do the same.
Goodell showed a bit of leniency Monday, saying in a statement if Payton, Loomis and Vitt "embrace the opportunity and participate in a constructive way," he would consider reducing the financial penalties on them. None of them has been fined, but each will lose significant amounts while not being paid their salaries during the suspensions. Payton, who twice apologized for his role in the bounties, could lose more than $6 million.
Goodell added he would consider modifying the forfeiture of the team's 2013 second-round draft choice, perhaps to a lower round. But New Orleans still will receive a draft penalty next year and will lose this year's second-round pick.
While the Saints await punishment for some players, they have the not-so-small task of finding an interim coach to replace Payton. They have talked to Bill Parcells, Payton's mentor since their days together in Dallas, about coming out of retirement.
Parcells, who turns 71 in August, has said he would consider coaching the Saints if asked to help his former protege. Parcells won two Super Bowls with the New York Giants and took the New England Patriots to a Super Bowl, but has not coached since retiring from the Cowboys after the 2006 season, though he then worked in Miami's front office.
If the Saints were to hire Parcells or anyone from outside the organization, the club would have to interview a minority candidate to comply with the NFL's "Rooney Rule."
Vitt also could be a candidate to step in, as he did briefly last season when Payton broke his leg, once his suspension ends.
Because Loomis can remain as GM until late summer, he will oversee the draft in late April and handle other roster moves. Loomis had been told by Saints owner Tom Benson to ensure that the bounty program was dismantled, but did not act.
AP Sports Writer Brett Martel in New Orleans contributed to this report.