However, lower order cameos from Mark Boucher (19) and Albie Morkel (19) ensured South Africa ended their 20 overs with a competitive total.
And after having their opponents 66-5 from 14.1 overs, Paul Collingwood's men were chasing 126 for victory after late blows from JP Duminy and Albie Morkel.
Ramnaresh Sarwan and Daren Ganga made half-centuries, but Albie Morkel supplemented his century with figures of 3-48 to keep the Windies in check.
"Neil McKenzie plays this four-day game and then goes home, and then we're joined by Shaun Pollock and Albie Morkel for the Twenty20, " said Benkenstein.
Australia's prospects of building a defendable total ended when all-rounder Hopes drilled a lofted drive off Albie Morkel to Neil McKenzie at cover in the 47th over.
Meanwhile, all-rounder Albie Morkel, brother of Morne, will replace injured fast bowler Lonwabo Tsotsobe in South Africa's 12-man squad for the second Test, which starts in Durban on Friday.
Ravi Bopara had made five when he was dropped at slip by Albie Morkel, but he also failed to take advantage of the reprieve, running himself out for 23.
Reserve wicketkeeper Morne van Wyk was a surprise inclusion ahead of the vastly experienced Mark Boucher while others to miss out included Albie Morkel, David Miller and Rusty Theron.
Skipper Johan Botha made 23 off 15 deliveries, while Albie Morkel finished on 32 not out when he hit the last ball of the innings from Syed Rasel for six.
Neil McKenzie, Paul Adams, Albie Morkel, Ashwell Prince and David Terbrugge have all been dropped following a disappointing tour to New Zealand earlier this year and Gary Kirsten has retired.
Not even some lusty blows from Mark Boucher (37 not out), who lifted Hilfenhaus for a huge six in the last over, and Albie Morkel could prevent South Africa from finishing short.
Kevin Pietersen crashed boundaries off his first two balls but hit an Albie Morkel full toss down to Roelof van der Merwe at mid-on, and the fielder dived to his left to take a stunning catch.
Patel, bowling in the rather luxurious position of South Africa needing nearly eight runs an over, soon removed Boucher, and then caught Albie Morkel off his own bowling immediately after being swatted for two sixes by the same batsman.
Pakistan stuttered a little to be 68-3 in the 17th, but Yousuf played a patient innings, Shoaib Malik added an important 42, and Misbah-ul-Haq (29 not out) supplied the winning hit with a massive six over long-on off Albie Morkel.
Michael Beloff QC, the man who chaired the Code of Conduct Commission that rejected those appeals, will chair January's full hearing against the trio along with fellow code of conduct commissioners Justice Albie Sachs of South Africa and Kenya's Sharad Rao.
Hafeez and Farhat took their time initially but gradually accelerated to post a century partnership from only 123 balls as the home side had cause to rue JP Duminy's failure to hold the early chance offered by Hafeez from the bowling of Albie Morkel.
BBC: SPORT | Cricket | International Teams | Pakistan | Pakistan openers hit form on tour
Albie Morkel injured his leg after a collision with Vaughn van Jaarsveld chasing a top edge in the deep but it not dampen South African spirits, which were soon lifted again as the amiable Tsotsobe appealed for a return catch from Johnson almost as an after-thought, replays confirming a clear dismissal.
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