South Africa had been scheduled to play in the competition with Pakistan and Sri Lanka from April 1 to 10.
"We value our players and officials and we cannot continue with the tour when there is concern about their safety," Gerald Majola, chief executive of the United Cricket Board of South Africa (UCBSA), said in a press statement.
"We received an advisory from the Department of Foreign Affairs informing us not to travel to the Gulf region under the current circumstances prevailing there.
"We are, however, engaged in discussions with the tournament organisers as to possible alternative venues and or dates for the tournament to be held," Majola said.