New Zealand got a flying start to lead 20-3 at half-time as Jordan dazzled.
He created the opening try after just five minutes by jumping to his feet quickly after a tackle, carving through the defense to put Smith over for a converted try.
Mo’unga extended New Zealand’s lead with a penalty.
The Springboks barely saw the ball in the opening quarter of an hour as the All Blacks enjoyed more than 90 percent possession.
Jordan again made inroads up the middle before sending the ball wide where Frizzell bulldozed over South Africa full-back Willie le Roux to cross for their second try.
South Africa thought Kolbe had scored after an aerial tussle out wide with Beauden Barrett, but the referee judged the ball was knocked on.
Scrum-half Faf de Klerk landed a penalty as the Springboks needed 35 minutes to claim their first points before Mo’unga slotted a second penalty just before half-time.
New Zealand skipper Sam Cane failed to start the second half due to injury, replaced by Dalton Papali’i with No 8 Ardie Savea taking over the captaincy.
De Klerk also went off injured, with what appeared to be a knee injury, early in the second half.
South Africa grabbed their first try shortly after replacing their front row when replacement hooker Marx was muscled over by his pack on 53 minutes.
Kolbe then dived over in the corner for South Africa’s second try inside eight minutes, after Le Roux’s superb long pass cut out several defenders.
Jordan then touched down in the corner for his 22nd try in as many Tests when he juggled the ball from Barrett’s kick.
Mo’unga ghosted through the defence from a scrum for the All Blacks’ fourth try, before Smith’s late touch-down for South Africa.
New Zealand face Australia away in a fortnight, in their final championship game, the same weekend South Africa hosts Argentina.
New Zealand and South Africa meet again at Twickenham on August 25 in a pre-Rugby World Cup friendly.but in all Newzealand 35-20 South Africa.