Unable to find his permission slip to join the rest of Springfield Elementary on their afternoon trip to the chocolate factory, Bart Simpson is consigned to the numbing task of licking envelopes in the office of Principal Skinner. As he does so, the wall clock ticks slowly and tortuously towards 3pm and the end of the school day. Losing momentum with every stroke, it eventually begins to tick backwards.

Something of Bart's interminable wait ensnared Australia on the second day in Port Elizabeth, as they were frustrated and ultimately brought to heel by a South African side well attuned to playing Test matches at the kind of deliberate pace unfamiliar to, and unloved by, the touring captain Michael Clarke and coach Darren Lehmann. Graeme Smith's men cannot afford to lose this Test, and on a pitch where application and determination can be enough to keep out most kinds of bowling, they pushed doggedly towards a position from where it was difficult to do so. Then, ball in hand, they swarmed over an opposition that chose precisely the wrong moment for a seaside siesta.

Australia did not do a whole lot wrong in the field, erring slightly in places but never transgressing so badly as to drop a catch or make a poor misfield. But they were slowly, gradually lulled into a sense that the game was going nowhere - never more so than when JP Duminy's batting partners Vernon Philander and Wayne Parnell soaked up 74 balls between them for 16 runs after lunch - and when asked to bat for 25 overs before the close showed the kind of inattention that can cost a Test match. Suddenly the clock ticking backwards was free-wheeling forward on South Africa's schedule.

The first day had been a good one for the tourists, given the minimal life to be found in the pitch. Central to their corralling of South Africa had been the harvesting of early wickets with the new ball, thanks to an excellent first spell by Ryan Harris and a decent one from Mitchell Johnson. Harris took the first over from the Park Drive End and Johnson followed up, downwind, from the Duck Pond End. So comfortable they had seemed at these ends that it was odd to see Harris and Johnson commence from opposite directions with the second new ball, particularly as the breeze had not shifted.

It might have been a minor issue, but the essential truth of the morning was that the ball did not swing, and neither Harris nor Johnson overly troubled Duminy or AB de Villiers. Given the narrow window for the ball to offer some assistance and the evidence of the first day, this was the sort of oversight Australia have seldom made in recent times under the guidance of Lehmann and the pace bowling coach Craig McDermott.

For the remainder of the innings there was little either coach could do, apart from encourage their men to keep things tight and be patient. If Duminy and de Villiers declined to push the game forward at any sort of proactive rate, they were also averse to making mistakes. Both strolled to centuries, while Vernon Philander and Wayne Parnell were less concerned with batting than occupation. These passages were torpid, straining the endurance of Australia's batsmen, who ultimately walked out to bat after tea with senses just slightly deadened by the experience of their longest stint in the field since Hyderabad in March 2013.

What followed was a chastening reminder of how the Australian top order is still worryingly erratic despite the team's recent success. Chris Rogers has not enjoyed South Africa to date, and was close to lbw against Dale Steyn before falling in the same manner to Philander - he would not have missed either ball during the rich vein of form he found late in the Ashes series. A short-term fix for those contests against England, Rogers is now under pressure for his place, particularly as Shane Watson regathers fitness.

Alex Doolan and Shaun Marsh fell to a high quality first over from Parnell, nibbling the ball around on his home pitch and coaxing a pair of edges from batsmen not yet set. Neither Doolan nor Marsh could be heckled too harshly for this, given their sturdy efforts at Centurion. But nonetheless it was a circumstance in which they needed to be fully alert, and in Marsh's case his edge ran from a bat angled in the manner of his India horrors rather than straight as it had been last week.

Briefly, Clarke and David Warner countered, their aggression consistent with that of Brad Haddin and Steve Smith at critical moments against England. But they were not in control of proceedings, as Morne Morkel in particular extracted previously unseen life from the pitch, using every inch of his gargantuan frame and high arm action. When the wicket fell it was not to be Morkel, who was most unlucky to have Warner dropped by de Villiers of all people, a swift delivery not settling into the gloves. Instead Philander celebrated Clarke's waft to short cover, the captain defeated not by an excess of pace but a lack of it.

Most troubling of all for Australia is the fact that Clarke is now in the midst of something like a batting slump, having gone eight innings since he last reached 25 - his first innings century at Adelaide Oval. In statistical terms it is a streak unmatched in his career, though he did also struggle mightily in 2010-11, immediately before taking over the captaincy from Ricky Ponting.

While winning arrived so handsomely, Clarke's thin run of scores looked as much a blessing as a curse, showing that Australia were not entirely reliant on his batting. Now however it does become a matter for some concern, against opponents glimpsing a way back into a series that looked beyond them only days ago. Without a significant rearguard over the next three days, it will be Australia stuck in the principal's office, wondering how they came to be gazing helplessly at the slow moving clock of the world's best team instead of enjoying the sweet tastes of a winning African excursion.