Stoinis was crowned the Big Bash League player of the tournament, but missed out on selection despite his 612 runs at an average of 55.63 for the Melbourne Stars during the 2019-20 campaign.
The 30-year-old will be on standby for both the ODI and T20 squads, who will each play three matches against South Africa in February and March.
“Marcus Stoinis is a standby player for each squad and was unlucky to miss out due to the makeup of the current top order,” Australia national selector Trevor Hohns said in a statement on Tuesday.
“It is terrific to have a backup player of his calibre in such good form.
“Of course there are other unlucky omissions which is always the case when selecting these squads.”
Maxwell returns after his exclusion from the ODI squad for last month’s matches against India, who won the series 2-1.
Mitchell Marsh, Jhye Richardson and Sean Abbott have also returned, the latter duo only part of the T20 squad.
“These are two very well-balanced squads with a focus on the specific skills each individual offers in their respective roles. The squads include returning players Glenn Maxwell, Mitch Marsh, Jhye Richardson and Sean Abbott,” Hohns said.
“It is fantastic to have Glenn back in both squads given his brilliant form in the middle order for the Stars along with his results with the ball. Glenn was one of the first picked in the most recent T20 team at the start of the summer, prior to his break from the game.
“The same can be said for Mitch. He has been in tremendous touch with the bat for the Scorchers since his return from injury and is now back bowling well. His performances warranted inclusion in the area he operates as a powerful middle-order batsman and handy bowler.
“Jhye Richardson also returns to the T20 side from injury with his performances demanding inclusion. He is a terrific young player who has been sensational in all forms of the game; and is an extremely strong fieldsman.
“Matthew Wade is also in red hot form with the bat. He is a very strong fielder; and a great person to have in any team. He can also substitute as wicketkeeper if required.”
The T20 series begins in Johannesburg on February 21 before the ODIs start eight days later.
Australia T20 squad: Aaron Finch, Sean Abbott, Ashton Agar, Alex Carey, Pat Cummins, Mitchell Marsh, Glenn Maxwell, Jhye Richardson, Kane Richardson, Steve Smith, Mitchell Starc, Matthew Wade, David Warner, Adam Zampa. Australia ODI squad: Aaron Finch, Ashton Agar, Alex Carey, Pat Cummins, Josh Hazlewood, Marnus Labuschagne, Mitchell Marsh, Glenn Maxwell, Kane Richardson, Steve Smith, Mitchell Starc, Matthew Wade, David Warner, Adam Zampa.
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