Maxwell has been named vice-captain of the four-day squad, a reward for his recent success as captain of IPL side King's XI Pubjab, in which he relished the added responsibility hitting 310 runs at a strike rate of 173.18.
The four-day side will play two matches against South Africa A from 12-15 July and 19-22 July.
Boland and Stoinis both feature in the one-day side, which will take part in a tri-series against both South Africa A and India A ahead of the final on 8 August between the top two finishing sides.
National Selector Trevor Hohns said: “We have opted for a well-balanced squad featuring some experience blended with younger players, with an emphasis on building our depth for the future.
“This is a great chance for these players to experience foreign conditions against a quality international sides and really test their skills.
“With an upcoming Test Series in South Africa early next year it is also an opportunity to impress with their performances and put their names forward for consideration.”
On selecting Maxwell as vice-captain, Hohns said:
“He [Khawaja] will gel nicely with Glenn who recently had some captaincy experience in the IPL and we believe will respond well to this extra responsibility.”
The squad will depart for South Africa on July 8.
Australia A four-day squad
Usman Khawaja (C)
Glenn Maxwell (VC)
Australia A one-day squad
Travis Head (C)
Australia A tour of South Africa - Fixtures
12 July – 15 July: Australia A v South Africa A at Tukkies
19 July – 22 July: Australia A v South Africa A at Senwes Park
26 July: Australia A v India A at Tukkies
30 July: Australia A v South Africa A at Groenkloof
1 August: Australia A v India A at Tukkies
5 August: Australia A v South Africa A at Tukkies
8 August: Tri Series Final at Tukkies