Addressing journalists in Pretoria, Ebrahim said: "We are recalling him [Coovadia] for consultation which suggests that after consultation he will go back to Tel Aviv. It's not a permanent recall."
Ebrahim said that a South African who was part of the flotilla had been released from Israeli detention.
"Ms Gadija Davids was in fact on one of these flights arranged by the Turkish government that left Tel Aviv late last night and will in fact tomorrow be landing in South Africa," he said.
Yigal Palmor, an Israeli foreign ministry spokesman, said that his country regretted the South African announcement.
"Those who criticize Israel would be better advised to turn their criticism against the terror-supporting rioters from the flotilla, who have nothing to do with humaneness," he said.
South Africa is the latest of several countries to take diplomatic action against Israel over the raid.
The nine activists killed in Monday's pre-dawn raid on the Mavi Mamara were all Turkish or of Turkish origin.
Ankara has strongly condemned Israel's actions, cancelling joint military exercises and withdrawing its ambassador to Israel.
Nicaragua suspended all diplomatic ties with Israel on Tuesday.
Rosario Murillo, communications chief for Daniel Ortega, the Nicaraguan president, said her country's position "underscored the illegal nature of the attack on a humanitarian mission in clear violation of international and humanitarian law".
Stockholm also summoned Israel's ambassador to Sweden to demand an explanation for the attack, which it called "completely unacceptable", as eleven Swedish nationals were travelling in the aid convoy.
Israel claims it killed the activists in self defence, citing footage of soldiers being hit with poles and one being thrown overboard.
The UN Security Council has called for an impartial inquiry into the raid which took place in international waters. The call was rejected by Israel.