New South Wales and Sydney Sixers coach Bayliss has been called in to give head coach Darren Lehmann a week's break to prepare for the Test series against India and the ICC World Cup, both in Australia.
The T20 matches against South Africa in early November fall just days after Lehmann returns from a tour against Pakistan in to the United Arab Emirates.
"With Lehmann in the UAE focused on the Test matches, we have appointed Trevor to focus on the Australian T20 team to give them the best chance of winning the T20 international series against South Africa," CA team performance manager Pat Howard said.
"Darren will have had the Zimbabwe tri-series and the UAE tour against Pakistan in quick succession immediately before the biggest-ever summer of cricket in Australia, so it's important he has some time to prepare for each series."
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Lehmann said that while he wanted to coach every match the Australian team played, planning and preparation was critical to successfully manage the next 18 months for his team.
"We've got an absolutely huge period coming up. As soon as the tour to Zimbabwe starts in late August this year, we won't then finish until after the 2015-16 Australian summer in March 2016. It's pretty much non-stop," Lehmann said.