SA Rugby has reportedly made a request to World Rugby to investigate Australia's injuries that led to uncontested scrums after the Wallabies lost all three props - Angus Bell, James Slipper and Alaalatoa - during the match.
Bell suffered a cut above his eye and Alaalatoa failed a head injury assessment (HIA), with both not returning after halftime. Slipper then also suffered a head knock.
Match officials deemed the lack of props meant it was no longer safe to continue with contested scrums.
Slipper's exit occurred just after Springboks coach Rassie Erasmus turned to the "bomb squad" - bringing on Rugby World Cup-winning forwards Ox Nche and Malcolm Marx - leading to the allegations.
The South Africans still triumphed easily, running over the top of the Wallabies in the second half for a 30-12 scoreline.
Ahead of their second Test against the Pumas in Argentina, Alaalatoa said his team wanted to scrum against the world No.1 side and considered it a strength.
Indeed, the Wallabies' scrum success rate in the tournament is 95.7 per cent, exactly 10 per cent higher than the Springboks.
"Do they think I was trying to fake an HIA or something?" Alaalatoa asked after being made aware of the report.
"Mate, we want to scrum, that's what we want to do, especially as front-rowers, and that's a game where you want to take on that challenge, you don't want to shy away from that.
"We're at a stage in our team where we want to keep growing and keep fronting up against the best, so you never want to shy away from that."
Among the players to have led the Wallabies this year, Alaalatoa said he'd never seen a run of injuries like it in his 72 Test caps.
With replacement hooker Josh Nasser also forced off, leaving the team temporarily with 14 players, coach Joe Schmidt described the situation as "bizarre".
"I remember Joe (Schmidt) at the end of that game saying he's never been a part of that game where things like that have happened, and I don't think I have as well," Alaalatoa said.
The Wallabies take on the Pumas in Santa Fe in northeast Argentina looking for back-to-back victories after a 20-19 thriller in La Plata.
Alaalatoa said the tourists took some confidence from a win over the Pumas, who shocked New Zealand in the opening round, pleased with their patience and endeavour.
He said their poor restarts throughout the match had been a focus for improvement at training this week.
"That's definitely an area of growth for us," the 30-year-old Brumbies skipper said.
"Maybe the weather had something to do with that, but also a communication thing between the (forward) pod and our wingers there, but definitely an area we need to improve."
