Labuschagne scored 0 and 4 in the Test decider at Newlands as Australia slipped to a 176-run defeat and 2-1 series loss, making it 16 Test innings without a half-century at average of 23.66 for the number 3.
The 32-year-old was already under immense pressure to keep his place in side before the South Africa tour, with former Australia international Simon Katich suggesting that keeping him in the team could be damaging to his career.
McDonald did not respond to Katich's comments directly but suggested that Labuschagne will find it difficult to keep his lace for the home series against New Zealand starting in December.
"What I can say is that any opportunity that you get to play for Australia, I don't think damages you," McDonald said. "I think there's even been critiquing of some of our younger players where they've been placed and the harm that that may cause to their careers and things like that.
"We believed in Marnus for this tour. We'll have to reassess that as we move forward. Others will sit there and say what that means for him.
"There'll be a lot of speculation. There's still a very good cricketer there. Every time he drops back to state level, he outperforms the others.
"He's had some opportunities that he's missed on this tour in particular so that'll be something in the next week or so that we'll get our heads around. We're not in a rush to make decisions. There's too much emotion. But, as I said, he hasn't taken his opportunity on this tour."
There have also been calls in Australia for the Test side to regenerate, as ageing squad has now lost a Test match at home to Bangladesh and then a series defeat to the Proteas.
McDonald said the "right decision" had been made with Steve Smith withdrawing from the team at the last minute due to a an issue with his neck sustained earlier in the series.
"The day before, it looked really positive," McDonald said. "But you never know how you're going to pull up from that. All I'll say is, the medical team and Steve gave it every chance.
"He wasn't ready to play. He acknowledged that. We do put a lot of trust into our players, in particular, our senior players who know their body quite well. So that decision of Steve, I think, was the right decision.
"It's happened now. What do we need to do to make sure it doesn't happen again and give him the best preparation that we possibly can."
The Proteas blew Australia's batting order away on the fifth day of the deciding Test at Newlands, the visitors crumbling to 111 all out as the hosts wrapped up a 176-run victory and a 2-1 series win.
Steve Smith is expected to recover in time for Australia's opening Test against New Zealand in December after medical examinations ruled out significant damage to his neck.
Australia took the upperhand on the second day of the third and deciding Test against the Proteas at Newlands after the tourists went to stumps on 330-4, a lead of one runs with six wickets remaining.
The Proteas got off to a fabulous start in the third and deciding Test against Australia at Newlands, but the tourists hit back in the final two sessions as the home side were 329 all out.
