According to an ICC media release, match referee Andy Pycroft imposed the sanction after Heinrich Klaasen's side was ruled to be one over short of the target after time allowances were taken into consideration.
Pakistan opener Fakhar's score came from 155 balls and he hit 18 fours and 10 sixes to give South Africa a big scare in the second one-day international.
All-rounder Wihan Lubbe and fast bowler Lizaad Williams have received maiden call-ups to the Proteas side.
The matches are scheduled to be played from July 11-25 and will comprise three ODIs, that will form part of the ICC's Cricket World Cup Super League programme, and three T20 Internationals
The 32-year-old legspinner Zahid Mahmood picked up 3-40 in his debut game and had reduced South Africa to 65-7 before Miller's clean hitting powered South Africa to a total of 164-8
The all-rounder claimed five for 17 in four overs as the tourists restricted the hosts to just 144 for seven wickets after winning the toss and bowling.
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The three ODIs will be part of the ICC Super League, a pathway to ensuring direct qualification for the 2023 World Cup scheduled to be held in India.
Mohammad Rizwan enjoyed a brilliant outing for Pakistan in the first T20I against South Africa.
Rizwan became only the second Pakistani to score a hundred in all three formats.
Pakistan beat South Africa in a test series for the first time in 18 years with two emphatic victories at Karachi and Rawalpindi.
Hasan, who bagged five wickets in the first innings, tormented the Proteas again returning figures of 5-60 and South Africa collapsed to 274 all out after lunch on the last day.
Hasan Ali bowled an absolute ripper to dismiss South Africa's Rassie van der Dussen on the final day of the second Test in Rawalpindi.
Rizwan said he was not worried about the partnership between Aiden Markram and Rassie van der Dussen.
Pakistan won the first test by seven wickets and has not beaten the Proteas in a home test series since 2003.
Allrounder Faheem Ashraf and Mohammad Rizwan were dropped off successive deliveries before featuring in a 52-run sixth-wicket stand.
Temba Bavuma displayed an incredible fielding effort to dismiss Fawad Alam during the second Test between Pakistan and South Africa.
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De Kock, who was handed the Test captaincy on a temporary basis for the 2020-21 summer, hasn't been in good form, scoring just 15 and 2 in the two innings.
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