• Points from the matches, which affect qualification for the 2023 World Cup, could now be awarded to Australia.
• South Africa sit 11th in a 13-team qualifying league while Australia are eighth, which is the final automatic qualifying place.
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South Africa have withdrawn from a one-day international series in Australia next January because it conflicts with a new domestic T20 competition.
Cricket Australia refused a request to reschedule the three-match series.
Points from the matches, which affect qualification for the 2023 World Cup, could now be awarded to Australia.
Pholetsi Moseki, CEO of Cricket South Africa, said: “The sustainability of our new T20 League is reliant on having all our domestic players available.”
The International Cricket Council must decide how to allocate the points from the matches, which count towards automatic qualification for the next ODI World Cup in India in autumn 2023.
South Africa sit 11th in a 13-team qualifying league while Australia are eighth, which is the final automatic qualifying place.
Countries that fail to qualify directly will have to fight for the remaining two places via a further tournament.
South Africa will play three ODIs against England in July as part of a summer tour that also includes two one-day internationals against Ireland in Bristol in August.
Meanwhile, Meg Lanning says Australia's players will relish the chance to complete a 'grand slam' of tournament victories at this month's Commonwealth Games.
Australia currently hold the women's Ashes as well as World Cups in both T20 and 50-over formats of the game.
A men's cricket event was played at the 1998 Games in Malaysia but this is the first-ever women's tournament.
"We're looking at it as a very unique opportunity. We want to win that gold medal," Lanning, 30, told BBC Sport.
"Our group is really excited about it. It's a new challenge, and I think it comes at a really good time for our team."
Australia won the T20 World Cup in 2018 and 2020 and retained the Ashes in February.
Lanning's side also romped to victory in the World Cup in April, defeating England in the final togo through the tournament unbeaten.
They are favourites to win the eight-team T20 tournament which will also feature England, New Zealand, South Africa, India, Pakistan, Sri Lanka and Barbados.
All the matches will be staged at Edgbaston from 29 July to 7 August and Lanning claimed Australia will thrive on the opportunity to be part of a multi-sport Australia team at Birmingham 2022.