South Africa managed through the 5.3 overs of cricket before lunch to be 0-11 at the break on Sunday, after rain delayed play by two hours and then returned 25 minutes later in Gqeberha.
Opener Marques Ackerman survived 14 dot balls from Josh Hazlewood on debut before scoring a single on the last before the break, while Aiden Markrm cover-drove Mitchell Starc for two boundaries on his way to 10no.
But the story of the day was Australia opting to bring Scott Boland into the side for Lyon.
Lyon has been overlooked twice when fit for pink-ball encounters in the past 18 months, but has played every daytime Test for Australia since July 2013.
But this is a significant change, with more grass left on a St George's Park wicket that is generally considered to be slow and friendly to spin.
Lyon has now missed five of the past 10 Tests for Australia through a combination of injury and selection, and bowled just two overs in Perth last summer.
The 38-year-old Lyon admitted he was "filthy" when left out of Australia's team against England for the day-night Test at the Gabba last year.
"(It's) partly conditions, and Scotty Boland has been incredible whenever he's played Test cricket," Cummins said at the toss.
"So it felt like it aligned this week and it was the right time to insert him.
"When there's anything in the wicket, he gets a lot of seam movement. He's super accurate, and even if it does flatten out he brings that control."
The signs Lyon wasn't playing were there on Sunday morning when he picked up a football during warm up, and appeared to congratulate Boland for his selection.
Australia also have the advantage of Matt Renshaw's off spin after his two wickets in the first Test win, along with Travis Head's tweakers and Beau Webster's ability to bowl off-breaks.
Lyon's omission was the only change for Australia, with Nic Maddinson to remain at the top of the order and Renshaw No.5 after his first Test heroics.
South Africa welcomed back pace spearhead Kagiso Rabada in place of spinner Keshav Maharaj, with fellow tweaker Simon Harmer holding his spot.
Ackerman's rise to open, meanwhile, comes after he had never done so at first-class level.
Matthew Breetzke, who has opened before, has also come into the side with Tristan Stubbs and Kyle Verreynne axed.
More rain is forecast across the opening two days of the Test, although the heaviest is predicted overnight.
A win at St George's Park will wrap up the series for Australia after their 214-run victory at Kingsmead Stadium last week, with the third Test in Cape Town next week.
"Any away series you want to win," Cummins said.
"They're not easy to come by, so we're in a good position, one-nil up, so we're going to give this one our best shot."
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