Malan faced 193 deliveries and hit just two fours as he first stitched a 71-run stand with opening partner Dean Elgar (34) and then shared a 52-run stand with Zubayr Hamza (18) before England's pace ace James Anderson removed the latter with a beautiful reverse swinging delivery that found the batsman's outside edge and sailed to wicketkeeper Jos Buttler in the penultimate over of the day.
Elgar, who slammed 88 in the first innings, was dismissed by part time spinner Joe Denly who had him caught behind after the Proteas started well in their pursuit of a daunting target.
Malan got to his 50 off 144 balls and never looked out of place in his first Test as he negotiated spin well and also saw off the challenge from Anderson and Stuart Broad early on with Elgar at the other end.
Earlier, resuming at 218/4, Ben Stokes launched a brutal assault while Dom Sibley made an unbeaten century to help the tourists declare at 391/8. Stokes smashed 72 off 47 balls, while Sibley got to his maiden Test hundred off 269 deliveries. His unbeaten knock of 133 was laced with 19 fours and a six.
Stokes and Sibley added 157 runs in just 32 overs before the declaration to fire England in a position of strength before Malan and Elgar dug deep and took the hosts to 46 for no wicket at Tea.
South Africa currently lead the four-match series 1-0 after winning the first Test in Centurion by 107 runs.
Brief scores: England: 269 all out & 391/8d (Dom Sibley 133 not out, Ben Stokes 72, Joe Root 61; Anrich Nortje 3/61); South Africa: 223 all out & 126/2 (Pieter Malan 63 not out, Dean Elgar 34)
( With inputs from IANS )
