The governing body made the decision after far-right Hindu nationalists stormed the Board of Control for Cricket in India offices in Mumbai.
Shiv Sena party activists threatened to prevent Pakistani Dar from standing in the fifth one-day international in Chennai on Sunday.
Dar is a three-time winner of the ICC's Umpire of the Year award.
"Under the present circumstances, it will be unreasonable to expect from Aleem that he will be able to perform his duties to the best of his abilities," an ICC spokesman said.
Shiv Sena blames Pakistan for militant attacks in India and is opposed to any engagement with it.
A member of the elite panel of ICC umpires, Dar officiated in the first three ODIs and was scheduled to stand in the fifth match in Mumbai on 25 October. South Africa lead the series 2-1.
A meeting between India and Pakistan's cricket board chiefs at the Wankhede Stadium was cancelled after the protests.
BCCI chief Shashank Manohar was scheduled to meet his Pakistani counterpart Shahryar Khan to discuss India's participation in Pakistan's home series in December.
Umpire Aleem Dar has been withdrawn from the India-South Africa series by the International Cricket Council.