Morkel's absence put further strain on the Proteas' pace attack, which battled through an opening day of fruitless toil against Australia batsmen Shaun Marsh and Steve Smith at Centurion.
Morkel's height made him one of the home side's more threatening bowlers on Wednesday, and if the injury sustained while fielding on day one is serious it would be a major blow to the hosts' hopes of taking out the three-Test series.
West Indies pace icon Michael Holding said in the lead-up to the match that Australia's fast-bowling depth is superior to the Proteas' stocks.
"Australia certainly have a bit more depth in their fast bowling attack," Holding said.
"We all know that (Dale) Steyn is a fantastic bowler. He's a great bowler, one of the best fast bowlers around. If not the best.
"(Vernon) Philander, he's not quick but he's a good bowler. He takes a lot of wickets.
"Morkel is a good bowler.
"But those three are who everyone depends on.
"They're OK, but if they ever have a problem - say with injury - they're going to struggle."
Steyn was the pick of the Proteas' bowlers on day one and claimed the scalps of Michael Clarke and David Warner, but he was well down on pace due to a stomach bug.
"He had a bit of diarrhoea overnight. It was a serious effort from Dale today," Proteas allrounder Ryan McLaren said of Steyn.