Players began flying out of South Africa on Sunday and Monday, with Australia to now turn their focus to a home series against New Zealand and a tour of India that starts in January.
There remains an ongoing sense of frustration about the way the South Africa tour ended, with McDonald lamenting a number of missed opportunities to clinch the series.
That includes letting South Africa off the hook with the ball in Gqeberha and Cape Town, while nightmare collapses in both those Tests also hurt.
Australia have been 4-95 or worse in 14 of their past 25 Test innings, with that brittleness exposed again as they slumped to 8-62 on the series-deciding day five in Cape Town.
But Australia's coach pointed to the performances of Cameron Green, Matt Renshaw and Josh Inglis as reasons for legitimate positivity, with the latter two scoring centuries.
"If you look at the batting unit, I think we walk away in a stronger position," McDonald said.
"For Josh Inglis to step up at late notice (in Cape Town) ... he's been a batter that's been carried around with us for a while, it's exciting.
"Albeit there's a lot of negativity floating around at the moment, it's exciting to see him and Cameron Green and even Matthew Renshaw."
McDonald also admitted selectors would have some decisions to make "around the age profile of that team", with 23-year-old Cooper Connolly playing his second Test in Cape Town and Sam Konstas firing in the Sheffield Shield.
"It's still a very good cricket team with a lot of very good players in there, and down the path they will be acknowledged as legends of the game," McDonald said of the current side.
"So we've got to balance that out with who comes in, what the next decisions are.''
Beyond the obvious turning points, McDonald pointed to Australia's inability to build a big first-innings lead in Cape Town after starting day three at close to parity with four wickets down as a big moment in the series.
But he stressed that not all fault lay with the batters, after the bowlers failed to put a final nail in South Africa on day four in Cape Town.
Australia have now lost three of their past five Tests, with the back-to-back defeats in Gqeberha and Cape Town the first successive failures since the 2023 Border-Gavaskar Trophy.
The defeats have cost Australia the No.1 spot in the rankings, ahead of a nine-month period that includes away Border-Gavaskar Trophy and Ashes series.
Still, McDonald pointed to Pat Cummins' 60 per cent win rate as skipper and the fact it is one of the highest among all Australian captains.
"We've underachieved here," McDonald said.
"It feels as though it's hard to win on the road. That's the greatest challenge, and that's where we will be critiqued.
"And we're incredibly frustrated that we weren't able to execute this tour after being 1-0 up."
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