The dispute caused the entire squad to sit out a game on Sunday and was an embarrassment to the South African soccer association and a country bidding to host the next Women's World Cup in 2027.
It was also another indication of the long-standing issue of pay disparity between men's and women's soccer.
South African soccer association president Danny Jordaan, whose organization came under stinging criticism over the last few days for not looking after its women players, conceded there was still "a massive gap" globally when it came to pay for men and women players despite world body FIFA's efforts.
To end the South African problem, the Motsepe Foundation gave $320,000 to be shared between the 23 players going to the Women's World Cup, officials announced at a press conference in Johannesburg. They said that had ended the standoff and would allow the players to travel in two groups later Wednesday and on Thursday to New Zealand ahead of the World Cup.
The players are also due to earn an additional $30,000 each in appearance money from FIFA.
The amount of money was not the only problem that caused the South African players, who are the reigning African champions, to challenge their national association over their treatment.
The South African players' union, which represents soccer players' interests, said this weekend that the players had no proper contracts or written agreements stating exactly what they would be paid to play for their country at the World Cup.
"Clearly the issue of contract negotiations started too late," Jordaan said.
The players were also angry that their sendoff game ahead of the Women's World Cup was staged at a small, little-known stadium outside Johannesburg, which is not good enough to host men's league soccer games in South Africa but was deemed fitting for the women's African champions.
The players' disgruntlement led them all to boycott Sunday's game against Botswana, forcing officials to field a makeshift team that included a 13-year-old girl to honor the fixture. The team, which was South African by name only and made up of players brought in last-minute from local clubs, lost 5-0.
South Africa's treatment of its women players was thrust into the limelight last year when former national captain Portia Modise, who was nominated for FIFA's world player of the year award in 2005, spoke about how she was sometimes paid $20 a game to play for the national team. She claimed she was living in "a shack" while playing for South Africa at times during her career.
Modise retired in 2015 after 15 years on the South Africa team. She played more than 120 games and scored 101 international goals.
"At the end of the day, they abused me," Modise said.