Quoting a Pakistan Cricket Board official, The Dawn reported that the mercurial pacer and Woolmer have been called by team manager Talat Ali after the third day's play.
The heated exchange allegedly took place after Woolmer made some comments about Shoaib's fitness during a training session, which the pacer did not like. The two argued on the ground and the tension continued in the dressing room as well.
The duo allegedly 'squabbled' and senior players had to intervene to prevent the matter from getting out of hand.
Shaoib is unlikely to play any part in the ongoing second Test at Port Elizabeth after picking up a hamstring injury yesterday.
The PCB official said the board was still awaiting a report on the bowler's injury.
''Shoaib is going through some medical tests at the moment and the nature of the injury will only be determined after getting the medical reports. It is premature to say how many days will the pacer require to recover because the reports have not come yet,'' he said.
Shoaib took 4-36 in South Africas first innings.