South Africa failed to pass 250 runs in either innings at the Sheikh Zayed Stadium and new coach Russell Domingo called it "a soft performance from the batting side".
Pakistani coach Dav Whatmore said he was not surprised by the win despite an upset loss to Zimbabwe last month.
"I knew that we could be competitive in different conditions and with a slight change of personnel. We gave a good competitive effort over the four days," Whatmore told reporters.
