Opening batsman Warner, the Test vice-captain, steps up to lead Australia in the T20 games which come a few weeks before the four-Test series in South Africa.
"The South African series is a very important one and we have made no secret of our desire to improve our record away from home," chief selector Trevor Hohns said today.
"As such we wanted to ensure the players had the best possible preparation and that means playing the tour match prior to the first Test."
"David is a very capable leader and has captained in Steve's absence before and done a fine job.
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"We wanted to ensure the T20 side had key leadership throughout this series and we know the team is in good hands with him at the helm."
There will be no other Test players in the T20 series and Glenn Maxwell returns to Australia's side after being passed over for the current one-day internationals against England.
"With some players currently injured and our frontline quicks heading to South Africa it gives a great opportunity to some of the young pace bowlers who have been selected to make their mark on the international stage."
Selected in the T20 squad for the first time are Sydney Sixers fast-bowler Ben Dwarshuis, Adelaide Strikers wicket- keeper Alex Carey and Hobart Hurricanes D'Arcy Short.
"Ben gives us good variety in the attack with his left- arm pace and has bowled particularly well with the new ball in the Big Bash League," Waugh said.
"D'Arcy's selection speaks for itself, he is the leading run scorer in the BBL and has also taken valuable wickets when handed the ball.
"He is in outstanding form and we look forward to seeing what he can bring to this T20 side."
Chris Lynn has also been included in the squad and is tracking well in his return from a calf injury.
Australia squad - David Warner (capt), Aaron Finch, Ashton Agar, Alex Carey, Ben Dwarshuis, Travis Head, Chris Lynn, Glenn Maxwell, Kane Richardson, D'Arcy Short, Billy Stanlake, Marcus Stoinis, Andrew Tye, Adam Zampa.