Captain Alun Wyn Jones, back row Ross Moriarty and fly-half Dan Biggar have given Wales fresh fitness concerns for the autumn internationals.
Earlier Biggar limped off during Northampton's English Premiership defeat by Leicester.
The 32-year-old fell heavily in a first-half challenge and came off at the break.
Jones led his team against the All Blacks, but took a blow to the same shoulder that he damaged in the British and Irish Lions' warm-up Test against Japan in the summer.
On that occasion the Ospreys lock staged a remarkable recovery to join the Lions ahead of the 2-1 series defeat against the Springboks and the results of his scan will be keenly awaited by the Wales coaching staff.
Dragons back row Moriarty has a potentially serious shoulder injury from the tackle that saw New Zealand's Nepo Laulala sin-binned.
"Ross has an AC [acromioclavicular] joint [injury]," said Wales head coach Wayne Pivac.
"He's was in quite a bit of pain. He's in pain relief at the moment. So it doesn't look too good.
"Al [Jones], talking to him in the changing room, he feels pretty good. He'll get a scan as a precaution.
"He's not in any discomfort. At the time, with the previous episodes, he couldn't play on. But he's feeling a lot better so that's a plus."
On the prospect that Jones had suffered another shoulder dislocation, Pivac added: "Certainly that wasn't the discussion and our medical team was in South Africa.
"I don't think they'll write him off after South Africa. We'll get a scan and we'll know a lot more come Monday."
Wales face South Africa on Saturday, 6 November with Jones, Moriarty and Biggar's fitness in the balance.
Biggar was not available to play for Wales against New Zealand on Saturday because the match fell outside World Rugby's official autumn international window.
But he could now be a doubt to face the Springboks in Cardiff next Saturday.
Gareth Anscombe was picked to start for Wales against the All Blacks with veteran Rhys Priestland on the bench.
Callum Sheedy of Bristol will also link up with the Wales squad before their encounter with the Springboks.
Recently-recalled flanker Thomas Young also came off at the break for Wasps at Bath on Saturday.