With talks between the union and the governing body deadlocked, around 230 players were left effectively unemployed when the previous five-year pay agreement expired at the end of last month.
The Australian Cricketers' Association (ACA) held an emergency meeting in Sydney last weekend and the players decided they would boycott the "A" tour unless a new Memorandum of Understanding (MOU) was signed this week.
"It is with great frustration that with no progress towards resolving the current dispute, Australia A players confirm they will not tour South Africa," the player's union said in a statement on Thursday.
"By making this call, the Australia A players have sacrificed their own ambitions for the collective; an incredibly selfless act that shows their strength and overall commitment to the group.
"All players are deeply disappointed at the behaviour of CA which forces this course of action, given the players would rather be playing for their country."
Cricket Australia released a statement expressing its own disappointment and said it had informed Cricket South Africa of "the players' decision".
"Cricket Australia regrets that players have made this decision despite progress made in talks between CA and the ACA in meetings over the past week," it read.
"While a new MOU has not yet been agreed, CA is of the view that these talks should have enabled the tour to proceed as planned."
At the heart of the acrimonious dispute is Cricket Australia's insistence that the two-decade-old model, under which players get a fixed percentage of revenue, should be jettisoned.
Cricket Australia believes the revenue-share model is unfit for modern times and is starving grass-roots cricket of funding, while players say it has underpinned the game's growth and prosperity over the past 20 years.
The ACA said on Thursday the governing body had refused mediation or to "offer any genuine flexibility" in negotiations and called for "common sense to prevail" with CA chief executive James Sutherland becoming directly involved in talks.
CA countered by saying that this week's talks had included "regular communication between CEOs".
The "A" team, captained by test batsman Usman Khawaja, were scheduled to play two four-day matches and a 50-over tri-series against India and South Africa on the tour.
Cricket Australia said the cost of the tour, which was estimated at around A$250,000 ($189,650.00), would be donated to a scheme to provide better and more inclusive cricket facilities around the country.
The senior Australia team is scheduled to play a two-test series in Bangladesh in August and September before some one-dayers in India and then the Ashes at home against England.
($1 = 1.3182 Australian dollars)
(Reporting by Nick Mulvenney, editing by Rory Carroll)
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