Jones, who led the Wallabies to the 2003 World Cup final, has been invited by Springboks coach Jake White to spend a week with the South African squad just six weeks before the tournament gets under way on September 7.
Earlier this week, O'Neill revealed he was both disappointed and perplexed by Jones' decision to accept White's offer.
"It's not something you would expect of a former Australian coach," he told Sydney's Daily Telegraph.
"In a sense it tells you the game has changed and coaches will take on jobs driven by other motives other than loyalty and patriotism.
"This is a quite definitive eyes-wide-open move by Eddie to go and advise the Springboks, amongst other things, on how to beat the Wallabies."
But Jones has now defended his decision to assist with the preparations of one of Australia's key rivals.
Speaking from South Africa's training camp, Jones said: "John [O'Neill] is entitled to his opinion, but it's a bit like the pot calling the kettle black.
"He went from being the chief executive officer of Australian rugby to being the chief executive officer of Australian soccer, which is a direct competitor. That was OK in his eyes."
Jones, who wore a Springboks tracksuit during his first day's training with the squad, explained that his job often required him to put patriotic feelings to one side.
"While you'll always have the softest part of your heart for the country where you were brought up, the fact is you move on if you have opportunities to coach in other countries," he continued.
"I have coached Japan and helped Tonga, Samoa and Fiji.
"If you look at soccer, Guus Hiddink coached Korea before the Socceroos. He also coached the Netherlands and he's now coaching Russia.
"That's four nations at the top level and I think rugby is moving that way. The reality is: I'm a professional coach."