Substitute Gerhard Steenekamp was the beneficiary of more forward dominance as the Boks barged over for their sixth try of the game.
Hendrikse rounded off the Bok scoring with his first Test try.
The Springboks will be well pleased with the results on their end-of-year tour. They conquered Scotland in Edinburgh, they swept south and vanquished England before going west to wallop Wales.
They did not always fire on all their cylinders, but it is perhaps a mark of their champion qualities that they did not need to. Their end-of-year tour, much like the preceding 10 Tests this year, was an exercise in building squad depth while winning.
The fact that they won 11 matches out of 13 this year will bring a smile to Bok fans, but coach Rassie Erasmus will perhaps be more pleased with the fact that he could use 52 players in the process.
Scorers
Wales (5) 12 - Try: Rio Dyer, James Botham. Conversion: Ben Thomas.
South Africa (26) 45 - Tries: Franco Mostert, Eben Etzebeth, Kurt-Lee Arendse, Elrigh Louw, Aphelele Fassi, Gerhard Steenekamp, Jordan Hendrikse. Conversions: Jordan Hendrikse (5)
Springboks slay Dragons in Cardiff
Image: Steve Haag Sports/Gallo Images
The Springboks' power, precision and at times poise proved too much for Wales as the visitors completed their end-of-year tour on a winning note in Cardiff on Saturday.
Despite a dip in the second half, they downed Wales 45-12 to seal their unbeaten status on the tour of the United Kingdom. It was their first unbeaten end-of-year tour since 2013.
The Boks condemned Wales to a record 12th straight defeat and though the Principality Stadium's roof was closed, it could not keep out more pall descending on Welsh rugby.
Left wing Kurt-Lee Arendse was electrifying with wing mate Cheslin Kolbe also flickering intermittently. Jordan Hendrikse played with confidence at first receiver, while Damian de Allende's impact was felt by the Wales midfield.
The Boks bossed the ruck in a way they had not on this tour and with a surfeit front football they were able to run onto the ball at speed.
A hulking Springbok running onto the ball at speed is one of the game's more compelling sights and the Welsh Dragon was like a deer in headlights.
Predictably Wales took a pounding in the scrum. Props Thomas du Toit and Wilco Louw were colossal with brother-in-arms hooker Johan Grobbelaar. By the time they departed the scene en masse (all 385kg), the Welsh scrum was in tatters.
The sight of Eben Etzebeth gingerly leaving the field in the 29th minute made for uncomfortable viewing, but RG Snyman typically brought energy and urgency.
A sign of the Springboks ' superiority was soon evident when their pace and power had Wales back-pedalling by the sixth minute. They hit the hosts with width and once they advanced down the right flank thanks to Cheslin Kolbe, the rapidly recycled ball was whipped to a speeding Franco Mostert who timed his run to perfection.
Mostert, who understandably looked short of a gallop when he returned from injury against England, was very much in the thick of things and it helped earn him the man of the match award.
Wales flyhalf Sam Costelow stood resolutely under the high ball but the Boks overwhelmed the hosts elsewhere. In fact, it was after Costelow gathered and went to ground that the Boks counter-rucked with purpose through Elrigh Louw.
From the turnover they hit left and soon there was the mesmerising sight of lock Etzebeth matching wing Kurt-Lee Arendse stride-for-stride down the left-hand touchline.
Arendse's return pass saw Etzebeth striding clear of the despairing defence. Wales were being caught off turnover ball, but perhaps more disconcerting for the hosts was the space they allowed the Springbok attack — criminally, even from first phase possession.
Arendse got in on the action when the Boks swept left from a line-out, leaving the spring-heeled winger in space. He used his sidestep to wrong-foot Costelow and dart in for the visitors' third try.
Imprecision, however, crept into the Bok game either side of the break. They weren't as clinical at the ruck as they were in the first half-hour, while their handling was less assured. They were particularly susceptible to spilling the ball in contact inside the visitors' 22.
Wales drew energy from that drop in Bok output. In fact, they closed the half chests bulging after they helped set up a try for Rio Dyer in the right-hand corner.
The Boks started the second half with intent but the errors continued to mount. They continued to bludgeon Wales up front but it took the deft skills of Arendse to unlock the hosts' defence. It was his delayed pass that drew hesitation in the Wales defence, allowing Aphelele Fassi to lengthen his stride towards the tryline in the 56th minute.
Substitute Gerhard Steenekamp was the beneficiary of more forward dominance as the Boks barged over for their sixth try of the game.
Hendrikse rounded off the Bok scoring with his first Test try.
The Springboks will be well pleased with the results on their end-of-year tour. They conquered Scotland in Edinburgh, they swept south and vanquished England before going west to wallop Wales.
They did not always fire on all their cylinders, but it is perhaps a mark of their champion qualities that they did not need to. Their end-of-year tour, much like the preceding 10 Tests this year, was an exercise in building squad depth while winning.
The fact that they won 11 matches out of 13 this year will bring a smile to Bok fans, but coach Rassie Erasmus will perhaps be more pleased with the fact that he could use 52 players in the process.
Scorers
Wales (5) 12 - Try: Rio Dyer, James Botham. Conversion: Ben Thomas.
South Africa (26) 45 - Tries: Franco Mostert, Eben Etzebeth, Kurt-Lee Arendse, Elrigh Louw, Aphelele Fassi, Gerhard Steenekamp, Jordan Hendrikse. Conversions: Jordan Hendrikse (5)
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