The responsibilities, as the general of the side, now rest on the shoulders of 20-year-old wunderkind Johan Goosen. "I always said I would do what was best for the team, and then individuals," Meyer said after he named his team on Wednesday for the game at Loftus Versveld on Saturday.
"It was especially tough to make the call with the game at Loftus.
"So it was a big call, but Morne is a true champion and he accepted it graciously."
Meyer's predecessor, Peter de Villiers, was in a similar position back in 2009 when pundits criticised him for not including Steyn. Steyn later stepped up to the plate in emphatic fashion against the British and Irish Lions, which kick-started his international career.
After 41 caps, and playing the role as saviour with his accurate goal kicking, his form started to dwindle this year. "He has put his body on the line for his country for the last three or four years and he won a lot of games that we could have lost if he didn't kick well," Meyer said.
"I just feel that it is in the best interests for Morne and the team that he doesn't play."
Goosen has played only 28 minutes in a Springbok jersey, after making his debut off the bench against Australia in Perth earlier this month. The youngster's long-range kicking and ability to attack the gainline has gained him a lot of supporters in his short career.
Lions utility back Jaco Taute is another rising star that could find himself thrown into the deep end against Australia. With Bok centre Frans Steyn still nursing an ankle injury, Taute could be moved into the starting XV at outside centre, with captain Jean de Villiers shifting back to his familiar position on the inside.
"The big question was to have two young players, especially with Frans Steyn not 100% fit," said the Bok mentor. "I would have loved to have two experienced guys on both sides of the youngsters, but I have a lot of confidence in them as well."
While Goosen is seen as more of a running flyhalf, compared to Steyn, Meyer cautioned that the public should not expect miracles from the youngster. "I think people have to be realistic because you cannot expect a 20-year-old to come in, win the game and score five tries, although I would love that," he said.
"There is also a process for Johan, he has been involved from the outset and we had chats when he was injured.
"But it is great as a coach to have depth at flyhalf, even though there is a long way to go before the next World Cup."
Meyer said he would make a final call on Steyn's availability on Friday. "It is such a crucial game and he is such an influential player," he said. "We were positive about him before training, but as he ran he hurt it [his ankle] again."
Meyer has also tinkered with his forwards, with lock Andries Bekker moving into the run-on side in the place of Juandre Kruger, and openside flanker Francois Louw replacing Marcell Coetzee, who shifts to the bench.
Prop Coenie Oosthuizen was included on the bench, while Elton Jantjies could finally earn his first Springbok cap if he comes on as a replacement. Utility back Juan de Jongh was bracketed on the bench in case Steyn failed his fitness test.
Springbok team: Zane Kirchner, Bryan Habana, Jean de Villiers (captain), Frans Steyn/Jaco Taute, Francois Hougaard, Johan Goosen, Ruan Pienaar, Duane Vermeulen, Willem Alberts, Francois Louw, Andries Bekker, Eben Etzebeth, Jannie du Plessis, Adriaan Strauss (vice-captain), Tendai Mtawarira. Replacements: Tiaan Liebenberg, Coenie Oosthuizen, Flip van der Merwe, Marcell Coetzee, Elton Jantjies, Jaco Taute/Juan de Jongh, Pat Lambie. – Sapa