"The way we performed in the Test series and in the ODI series it was very disappointing and to me it is an alarming situation for Pakistan cricket," he told the media after the team returned home today morning.
Misbah,39, said it was disappointing the way the team was whitewashed in the three-match Test series.
"We had gone there expecting to put up a close fight but a final three nil result caused hurt to all the players. We did better in the one-day internationals but that also we lost the final match," he said.
"It has been a tough tour and we will sit down and go through all the pros and cons of the tour and we need to learn from our mistakes. I think we also need to admit that South Africa was the better side than us," he said.
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Pakistan was whitewashed in the three test series and lost the five match one-day rubber by 2-3.
Misbah declined to comment on the future of senior players in the team or on the performance of some seniors.
"I think it is the job of the board and selection committee to guage everyone's performances also look into it in future," he said.
Misbah also rubbished reports that rift between him and Pakistan's T20 captain, Mohammad Hafeez had led to problems within the team and led to the disappointing results in South Africa.
"It is all rubbish and I have said this before everything is fine between us and in the team. Such rumors only tend to undermine the morale of the team," he said.