Pakistan's win levelled the series 1-1 with three matches left to play. South Africa had won the first match by 45 runs at the same venue on Thursday.
Match referee Alan Hurst of the Emirates elite panel of ICC match referees imposed the fines after Malik's side was ruled to be three overs short of its target at the end of the match when time allowances were taken into consideration.
And with the shortfall being more than two overs, Malik, as captain, was automatically charged with a level two code of conduct breach.
Malik missed most of South Africa's target chase because of cramps. Yunis Khan led the Pakistan cricket team during Malik's absence.
Hurst said: "The Pakistan team finished three overs short of the required number of overs, although they were fully updated throughout the innings of their progress by the umpires.
"And although captain Shoaib Malik was not on the field for much of the innings because of injury, he is still accountable in these circumstances," he added.
Malik was fined 50 per cent of his match fee for the breach and as he was found guilty, that punishment took precedence over any fine that was imposed on him as part of the Pakistan team.
The other players were each fined five per cent of their match fees for every over Pakistan failed to bowl in the time allowed. As a result, Malik's team mates were each 15 percent out of pocket following the match.