Kraft on Wednesday was critical of Roger Goodell's decision to uphold Brady's four-game suspension for his role in the Deflategate scandal, saying he was wrong to put his faith in the league during the appeal process.
When asked about those comments at the opening news conference of Cowboys training camp later Wednesday, Jones backed Goodell.
"He's got obviously a very tough job," Jones said. "Now I see some people doing that, that's that old violin that's not feeling too sorry for him because that's why you pay the big bucks is to deal with the big problems. But he's doing an outstanding job. I can tell you firsthand that in his spot you have to with people that you are counting on to help build and to help excel as far as the National Football League, I'm talking about the owners, you have to know that you're going to make some decisions that are very unpopular with that particular group. This is the case.
"I can speak to that because on a personal basis as well as for my franchise and our Dallas Cowboys franchise, we've had that happen to us. I'm sitting there living with the result of the commissioner's decision still today that I didn't agree with when it happened. And so some of the very people sometimes that have the biggest complaints, they're the ones who give you a phone call and say, 'Hey let's be a team player now and let's all get in here and realize that this happens to everybody and let's go on and compete. We've got a great league and a great game.'"
In 2012, the NFL stripped the Cowboys of $10 million in salary-cap space in part for how they structured the contract of receiver Miles Austin in an uncapped year. Even without a hard cap in place, the league felt the Cowboys circumvented league rules. The Cowboys and Washington Redskins, who were docked $36 million in cap space, lost their appeals and chose not to fight the cases through the legal system.
"He has to make hard calls," Jones said of Goodell, "and more often than not, you're going to have a season or you're going to have a period of time where those go against you as an owner in the NFL."
"I have a lot of confidence in Roger and the league offices," Ross said. "I dealt with them, as you know with our controversy not too long ago, and they're very objective. I don't have all the facts. I don't think any of us have all the facts. But I think the league takes everything into consideration, and I have a lot of faith in what the league ruled."
Ross said he understands how Kraft feels, having been in a similar situation.
"When it happens to you, everybody is always upset," Ross said. "It's a natural reaction. But I have a lot of confidence that the league has done the right thing. They have the facts, and I think Roger tries to treat everyone fairly."
The NFLPA filed motions Wednesday on Brady's behalf challenging the decision to uphold the suspension. The case was filed in U.S. District Court in Minnesota and assigned to U.S. District Court Judge Richard Kyle. The union had hoped for Judge David Doty, who historically has ruled in favor of players in labor cases against the NFL.
If Brady is not able to reduce the suspension via federal court, he would miss the Patriots' Oct. 11 meeting against the Cowboys at AT&T Stadium.
"I think Tom Brady is arguably as great a quarterback as we've ever competed against since I've been in pro football," Jones said. "And so the fact that he may not be there is substantive. I don't want to in any way say that the teams Bill Belichick puts together up there and Bob Kraft owns can't figure out a way to beat us without Tom Brady. If anybody can do it, they can do it."
Information from ESPN.com's James Walker was used in this report.