A panel voted 5-0 to uphold the ruling despite claims by Martin's attorney of sexual discrimination.
"Paternalism, male chauvinism, which sometimes manifests itself like, 'We've got to protect the women.' Well, you're protecting them out of their rights, and that's wrong," attorney Gloria Allred said during a press conference.
Martin's return to the ring has been remarkable. She was allegedly stabbed, shot and pistol-whipped by her own husband who had been her trainer.
"That 50th win meant more to me than anybody because it was my first fight without my ex-husband as my trainer," Martin said. "This just meant this win was for me. So it was stolen from me."
But fight officials said Martin stopped defending herself during the June 4 fight at Staples Center after breaking her hand in nine places and was at risk of substantial further injury if they allowed her to continue.
"She winced in pain, exhibited excruciating pain, turned her back on it and that's when I said, 'Stop, time,' brought the doctor in," said referee David Mendoza.
After hearing the referee's rationale for stopping the fight and testimony from the medical director of the world boxing council, the commission upheld the ruling.
"I will never be back in California to box again," Martin said. "I'm disappointed. Obviously, I feel that we proved everything that there was to prove. I was still defending myself. I was still winning the fight."
Martin said she didn't expect to win her appeal but had hoped the fight would be ruled no-contest.
"Women in sports and all men who care about supporting women in sports and in boxing, should be very concerned about the outrage that occurred today. It's completely an outrage," Allred said.
The 5-foot-4 Martin, arguably the best female boxer of her era, has stood out from other women fighters because she loves to trade punches, which got the crowd's attention. The fact that her slugfests often turned bloody was what really fired them up. She was a pioneer in women's boxing in the 1990s, once landing on the cover of Sports Illustrated.
The Associated Press contributed to this report.