The Proteas' maintained a tight line and their efforts yielded result when Jonathan Trott got out to Harris, trying to break the shackles.
Strauss just added two runs to his overnight score before Ntini struck to dismiss him for 46, leaving Eng at 98/2.
Kevin Pietersen and Paul Collingwood got together and tried to get England out of trouble as they went into lunch at 143/3.
Pietersen and Collingwood stuck around and started building a good partnership.
Just when the pair were looking good, Pietersen dragged a Morkel delivery onto the stumps, leaving England at 168/4.
Ian Bell was the next to depart, shouldering arms to a straight delivery from Harris.
Paul Harris was not finished yet as he went on to pick up the wicket of Matt Prior.
Amidst these, Collingwood went on to score his 17th Test fifty.
However, he departed soon after that, giving Harris his fourth wicket.
England were 242/8 when Swann and Anderson got together and put on a defying stand.
Swann went on to register his 4th test fifty - his first against South Africa.
Swann and Anderson put on a record stand of 106 before England were bowled out for 356.
Anderson got a wicket in the first over, dismissing Prince for a duck as South Africa ended the day at 9/1, leading England by 71 runs.