Smith's unavailability for the third Test and timeline around his injury remained a major talking point of the week, before Australia's fifth-day collapse and defeat on Saturday.
Cricket Australia revealed during the Test that Smith had undergone scans in Cape Town four days before the game, which showed joint damage.
After those scans, Cummins and Australia's coaches had indicated publicly Smith would likely still play, with the captain hoping the batter would "compartmentalise" the issue.
The 37-year-old then batted in the nets for 35 minutes the day before the game, before feeling he would not be right to take the field.
A pain-killing injection was then tried as a last-ditch bid to get Smith fit on the morning of day one, which ultimately left him with shooting pain and feeling worse.
Among Smith's concerns were an inability to flex his neck and therefore move his head forwards and backwards, as evidenced by his first-innings dismissal in Gqeberha.
Josh Inglis ultimately ended up scoring a first-innings century in Smith's place, before Australia collapsed to be all out for 111 on the final day and a 176-run loss.
"I obviously chat to him a fair bit and he wanted to give it right to the last minute. But he was feeling relatively good. He obviously had a few hits," Cummins said on Saturday.
"We were all really confident. We still knew he needed to pass a fitness test in the morning. It wasn't a dead certainty.
"But unfortunately, he just didn't feel quite right. He knows his body better than anyone else.
"I was definitely disappointed. He's the best player in the world, vice-captain, all those things.
"But the show goes on. And someone like Josh Inglis was lined up in case something happened. It was all good, we move on pretty quickly."
Cummins also insisted that Smith's absence did not impact his decision to bowl first on day one, and Australia would have done so anyway.
The call was heavily criticised as South Africa flew to 0-140 at lunch, before Australia had them all out at stumps for 329.
But batting last ultimately proved too difficult, with Proteas spinner Simon Harmer taking 6-16 and wreaking havoc on a heavily deteriorated pitch.
"It's hard to know, exactly," Cummins said, when asked if inserting South Africa had been the right call.
"You're always weighing up different things on this pitch. We knew it was going to be high-scoring.
"We probably thought it was going to be a little bit more on day one than it did. You don't win the toss and think you're going to bowl the opposition out for 100 or 200.
"But we thought if we could get 10 wickets on day one, that would put us right ahead of the game."
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