He was eventually caught behind off left-arm spinner Keshav Maharaj but even then had to suffer the indignity of waiting halfway to the pavilion while the umpires checked whether the ball had struck the wicket-keeper's helmet before being snaffled.
But it was the loss of Root sent England once again into a downward spiral and, although Jonny Bairstow stuck around to reach 45, Ben Stokes (0), Moeen Ali (18) and Stuart Broad (0) - all of whom played starring roles in the first innings at Lord's - failed to fire.
'It might be that the seamers play a bigger part this week, and that excites me, ' he said.
England may have won the first test by 211 runs, but the Proteas will back themselves to come back hard and try and win the second test.
The first-innings average in the last ten Tests at Trent Bridge is 295.
Broad, 31, suffered a repeat of his heel injury leading up to the First Test, but he was running in with speed and goal here.
However, he was let down by England's batsmen, who contrived to cede a 130-run first-innings advantage after they collapsed from 143 for three to 205 all out.
One of those pacemen, James Anderson, did not bowl much during Thursday's nets session, but Root insisted England's all-time leading Test wicket-taker was fully fit after struggling with groin and shoulder problems recently.
Root's attacking approach was his undoing, though, as he went for a full-blooded cover drive off Morkel and edged behind for wicketkeeper Quinton de Kock to take the diving catch that turned the day for South Africa.
England's batting line-up floundered in response, with openers Alastair Cook  and Keaton Jennings  removed in successive deliveries. His last four Test innings against England - all in England - are 61, 35, 52 and 19 not out.
At lunch, Root and Ballance, desperate to nail down his Test place after being recalled at Lord's, had taken England to 85 for two.
Anderson sent Vernon Philander back in the first over of play without adding to his overnight score of 54. In reply, South Africa lost only one wicket and are placed at 75 for 1.
He closed off the innings with Morkel's scalp to finish with his second fifer at Trent Bridge.
With him was Gary Ballance, who was 26 not out in an unbroken stand of 82. Kuhn faced 42 balls for two single-figure scores at Lord's, undone by a ideal Stuart Broad delivery in the first innings and perhaps a little unlucky to edge James Anderson down the leg side second time out.
An X-rated batting display from England means they are facing not only what appears an impossible fight to save this second Test but searching questions over the make-up of their top six for the remainder of this series.