The 45-year-old was dismissed by Ten Sports after viewers overheard him saying ''the terrorist's got another wicket'' when Amla took a catch to dismiss Kumar Sangakkara in the second Test between Sri Lanka and South Africa in Colombo.
Cricket South Africa said its switchboards had been jammed with complaints and that it would lodge protests with Ten Sports and the International Cricket Council (ICC).
''The ICC has strongly condemned racism and we will be discussing the matter with them,'' CSA chief executive Gerald Majola was quoted as saying.
A tearful Jones returned to Melbourne airport yesterday and said he was paying the price for a remark he thought he had been made during an advertising break.
''I waited four or five seconds and I just turned around and made a stupid, ridiculous off-the-wall comment that unfortunately was picked up in the background and as television people always know the microphone is always live,'' Jones told reporters.
''There was only one country in the world that didn't take the ad break live and that was South Africa. It was picked up by a few viewers.
''I wanted to make a full blown apology to Hashim Amla and the South African team so I wrote out a full page apology expressing my sincerest apology to all involved.'' Jones, who played 52 Tests between 1984 and 1992 with a batting average of 46.55, said he had apologised to Amla, a devout Muslim who is given dispensation not to wear any alcoholic beverage logo on his playing clothing.
''I gave him my sincerest apologies and he was gracious enough to accept it. He said I hope you get through this ugly situation that you are going through,'' Jones said.
He admitted the gaffe could cost him current and future contracts as a television commentator.
''I miss out on one Test day as well as seven One-day internationals so it has cost me a lot of money,'' Jones said.