His feet have been in a tangle all tour. The front one isn't moving freely enough and the back one is too often left behind. That has mostly resulted in him playing down the wrong line. On Saturday, they were more in sync, but only reluctantly so. What kept him at the crease was his defence, which is about as exciting to watch as someone building a 1000-piece puzzle. To the trained eye, there is something to be impressed with.
Cook can make everything look like an effort, especially the leave. When he hops back and watches the ball carry through to the keeper, there is a nanosecond of anxiety as Cook waits to see if he made the right call. His awareness of his offstump appeared so shaky in his first three innings on tour that it was difficult to believe Cook had spent more a decade-and-a-half opening the batting in domestic cricket.
The Cook who has bossed domestic cricket for the last seven seasons is not as much a stonewaller as the Cook who has been in Australia for the last four weeks. That Cook is more confident. This Cook is more circumspect, because he has to be.
Unlike many of his team-mates who have matured on the international stage - Quinton de Kock, for example, only played 10 franchise first-class matches before he made his Test debut - the bulk of Cook's experience has been at a lower level. That means most of the bowling he has faced has not been of the quality on display in this series. Of course, the South African first-class competition has the likes of Marchant de Lange in its ranks, but like any domestic tournament, there are also has less exceptional bowlers on the circuit.
Many players have spoken of the step up in intensity needed when they become internationals. it's been no different for Cook. This is only his sixth Test and even if he failed, its likely he would have been given a slightly longer run. In tough circumstances, he showed he deserves one.
Cook moved cautiously through an innings in which he lost partners at a quick enough rate to know that if he did not knuckle down, the Test could be gone. Slowly, he got into a rhythm of moving across his stumps to play Nathan Lyon into the leg side and getting forward to meet the fuller deliveries. He never looked entirely comfortable or in control.
On 45, after facing 96 balls, he edged Jackson Bird to the vacant second slip area. It could all have ended right there. On 49, after facing 113 balls, a Lyon delivery spun back to hit his thigh pad and carry to short leg. On 51, after facing 135 deliveries, Josh Hazlewood half-appealed for a lbw after Cook missed a flick.
But none of that unsettled him. Cook was content to let the dot balls mount. No doubt his father Jimmy's words - "You can get out to bad shot or a good ball, but you can't get out because you are tired" - would have been on his mind. He did not let the frustration or the fatigue get to him. Not even under lights, when legend has it that the pink ball becomes more difficult to face. He hung on, only just, but at the end of the day, he was still hanging on.
It was not supposed to be ugly. Especially not from Hashim Amla. The man with the magic wrists, the most delicate flick and smoothest drive in world cricket is supposed to make batting look like field of flowers. For his last four away series, that field has been razed to the ground.
Since August 2014, South Africa have toured Zimbabwe, Bangladesh, India and Australia for 10 Tests, and Amla has scored 233 runs at an average of 16.64. His top score is the 47 that he made in Hobart on this tour. In this period, Amla has been dismissed in single figures eight times and been caught behind (by the keeper or in the slips or gully) the same number of times.
Amla's issue seems to be that he is misjudging the line too often, something Josh Hazlewood, who has dismissed him all five times in the series, has taken note of. That could have changed when Mitchell Starc drew the drive but Matt Renshaw expected Matthew Wade to take the catch and reacted too late to hold on at slip.
That almost proved the catalyst for an Amla turnaround, as has so often been the case in the past. Amla attacked after that, with a drive, a cut and even a loft over mid-on for six, but Hazlewood ended all that when he got just the right amount of deviation to take the edge.
Part of Amla's problem could be that he is being called on too early because of the inconsistency of South Africa's opening pair. Eight times in the the 14 innings mentioned, Amla has walked in to bat with with the score less than 20. Some of those have been at No. 4, but since Faf du Plessis' took over as stand-in captain, Amla has been bumped up a place. Having spent most of his career coming in after Graeme Smith and Jacques Kallis, Amla had some buffer. Now, things have been different.
Amla was the speaker at the MCG press conference, the person who called the ball tampering allegations against du Plessis a "joke," and the one who reacted with feigned ignorance that sugary saliva could be used to shine the ball. Several players including du Plessis and the opposition captain Steven Smith have since confirmed that the sweet science is a common tactic. That has made Amla look as out of touch in his talk as he has in the middle.
But to write Amla off would be premature, especially now that Cook has come good. If Cook can find some consistency, some of the pressure may be pulled away from Amla and South Africa's top order can become beautiful again.