Neill, 35, was booed by a section of the Sydney crowd late in the game and turned to the grandstand and screamed, 'why are you f***ing booing?'
The incident capped a tumultuous few weeks for the skipper following constant media speculation over his position in the side.
"Towards the end of the game I think a few people had some courage juice and they started to boo me and only me when I was on the ball and I can't tolerate that," Neill said on Wednesday.
"I'm Australian coming to Australia to play for Australia and to be booed by Australians, it's unacceptable.
"But what it is, and these guys don't understand, it's detrimental to the team.
"We've got a lot of young guys who have put in an amazing performance last night, we were winning a game 1-0 against a team that's qualified for the World Cup and we've put in a display that's worthy of plenty of cheer and to here boos, it's unacceptable."
Neill admitted he was wrong to swear but is standing by his actions despite strong condemnation from former Socceroos including Robbie Slater and Mark Bosnich.
"I can apologise for swearing but we have to stamp that kind of thing out now because this is an exciting time for Australia and unfortunately it's tarnished what should have been an exciting and amazing night for Ange Postecoglou and the Socceroos and Australia," he said.
"It's just silly, it's disrespectful, we're all very proud Australians but we should all act the Australian way and that is to get behind each other and support the green and gold.
"It's an isolated incident, it's never happened before in my career, I hope it never happens again.
"I'm passionate about Australia and I'm passionate about what's happened last night, so there'll be no apology from me."
Get the best features, fun and footballing frolics straight to your inbox every week.
Thank you for signing up to Four Four Two. You will receive a verification email shortly.
There was a problem. Please refresh the page and try again.