Dale Steyn and Kagiso Rabada took four wickets apiece as Pakistan folded for 294 in their second innings at Newlands, Cape Town.
Faf Du Plessis scored a century while Temba Bavuma hit 75 as South Africa took a lead of 205 runs against Pakistan at the close of day two's play in the second Test.
South Africa finished day one of the second Test on 123/2, trailing Pakistan (177) by 54 runs at stumps.
Arthur was found to have violated Article 2.8 of the ICC Code of Conduct which relates to "showing dissent at an umpire's decision during an international match".
Faf and Sarfraz failed to open their accounts with the bat in both innings.
Amla's 63 not out guided the Proteas to victory but not without a series of scares.
But it was three rapid strikes by his fellow pace bowler Kagiso Rabada that turned the second day on its head in the final session.
Steyn's one wicket of the day took him to 422 in Tests and past Shaun Pollock as South Africa's leading wicket-taker of all time.
Steyn picked up his 422nd wicket against Pakistan in the Boxing Day Test match in Centurion as he sent back opener Fakhar Zaman in the seventh over.
Other specialist seamers in the squad include Mohammad Amir, Hasan Ali, and Shaheen Afridi.
DUBAI, United Arab Emirates: South Africa inflicted an innings and 92-run defeat on Pakistan in the second test on Saturday and preserved its seven-year record of not losing a test series away from home.Asad Shafiq
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