Jewish and Israeli groups have criticised the decision by the University of Johannesburg (UJ) to sever its ties with Ben-Gurion University of the Negev (BGU).
The South African university announced it would no longer work with BGU, following a long anti-Israel campaign by academics and intellectuals, including Archbishop Desmond Tutu.
The two institutions had enjoyed a 25-year partnership, working together on joint projects on water purification and research. But on Wednesday 60 per cent of the university's senate committee voted in favour of ending the relationship.
The move made UJ the first university in the world to sever ties with an Israeli institution.
Uri Keidar, the leader of the BGU student association, said: “I find it difficult to believe that BGU, the home of 20,000 freethinking students of different religious and ethnic backgrounds, is under this brutal attack."
Rivka Carmi, BGU president, said: "The only losers in this decision are the people of South Africa," while a spokeswoman for South Africa's Jewish Board of Deputies said such boycotts threatened freedom of speech.
Abraham Foxman, director of the Anti-Defamation League, said it was a “misguided and shortsighted” move.
“In demonising and rejecting BGU solely because it is an Israeli academic institution, this highly political decision does nothing to promote Israeli-Palestinian reconciliation and understanding.
“Moreover, it will deprive all South Africans of the new technologies being developed by BGU scientists to purify water.”