Dr Lewis said he opposed Dr O'Neill's call, but ended his protest to avoid a "s*** fight".
"I told him anything that happens from here is on you," he said.
He said the referee should have started counting to 10 as soon as Green dropped to the canvas and - if he failed to make the count - should have awarded him the win by disqualification if Mundine's shot was deemed illegal.
"It's set us back so many years," Dr Lewis said. "I thought it was disgusting. The referee should never work again."
Dr Lewis, who has been involved in the sport in various capacities for 45 years, plans to lodge an official complaint with the Australian National Boxing Federation and South Australian Office for Recreation and Sport boxing compliance officer Tom Hunter.
"It's made us a laughing stock around the world," he said. "They didn't take care of the boxer. If it happened in rugby league you'd be suing people.
"He (Green) couldn't punch with any power and he was huffing and puffing. He was fighting on instinct more than anything else. A heavy puncher, in the same weight class as Green, could have done serious damage."
Green's own assessment of his condition backs up Dr Lewis's diagnosis. "I was nearly knocked out cold," the West Australian told reporters in Perth on Monday. "It was a very, very hard thing to come back from, at any time in the fight."
Green revealed he was asked to repeat the doctor's name to prove he was capable of fighting on - and was allowed to keep going despite getting it wrong.
"I think I said the wrong name of the doctor anyway," he said. "There were two doctors, one was John O'Neill and one was (Lou) Lewis and I thought that was Dr John Lewis. It was enough. It got me going."
THE DECISION WAS WRONG
Dr Lewis also took aim at one of the judges who failed to dock Green a point for a foul in the seventh round.
American Steve Morrow scored the seventh round 10-10 despite the referee instructing judges to penalise Green for an errant elbow. "If he scores that round 10-8 like the other two judges, it's a majority draw," Dr Lewis said.
"This is something that should never be repeated again. Referees should be held accountable and so should doctors."
Mundine told The Daily Telegraph he wanted an official investigation into the blunder. "There has to be a proper inquiry," Mundine said. "That's what we're pushing for. There is an obvious mistake on one of the cards in round seven where a judge ruled the round 10-10 after Green had been penalised a point.
"That can't happen. The result should have been a majority draw. This was a disgraceful decision."
Mr Hunter said he did not have authorisation to speak to the media and directed news.com.au to Office for Recreation and Sport general manager Kylie Taylor.
In an email, Ms Taylor said the Australian National Boxing Federation was the sanctioning body for the event and the appropriate body to answer any questions.
News.com.au is still attempting to contact ANBF secretary Frank Hadley and Dr John O'Neill.
