Clarke finished the first day of the deciding match at Newlands on 92 not out with his team in the ascendancy on 331-3.
But he had to survive a series of painful blows from Morkel, being struck on the left forearm and the shoulder while also being felled by a blow to the cheek before being hit on the gloves.
Late in the day he was struck on the right thumb when Morkel was bowling with the second new ball.
"He could have tried to hit his way out of trouble but instead he went the other way and said, 'You can hit my body but you're not going to get me out'.
South African bowling coach Allan Donald also hailed Clarke's courage.
"Michael took a lot of blows for his team," said Donald.