Summary of Pakistan's tour to South Africa:
-Test series = South Africa won by 3-0
-ODI series = South Africa won by 3-2
-T20I series = South Africa won by 2-1
These results are not surprising considering that Pakistan batting line up has been on the decline for quite a while now, their only strength is their bowling. I have to be honest never expected Africa to do so well, considering their team is going though a transitional phase.
Honestly, most of the matches that South Africa won were way too close. South Africa won the last 2 T20Is by 6 and 7 runs, won a test match due to Azhar Ali not being able to play just 10 balls, got an unexpected advantage of rain in one of the ODIs and won it through Duckworth–Lewis–Stern (DLS) method by 13 runs, etc.
Overall, even though South Africa succeeded in winning the whole tour of Pakistan, I'd still not say that Pakistan played very bad. Both the teams played fine, but the South African team played a little better.
Overall matches were interesting and towards the end SA proved little better than Pak which helped them winning all the format matches. But Pakistan would be disappointed that inspite of coming so close they could clinch any of the series which would have helped them morally.