At its annual congress in Manchester, the motion was passed without debate and by a show of hands.
The motion follows last year's attempts by the union to implement a similar boycott motion, but was withdrawn by the Union following undisclosed legal advice.
This year's motion was debated despite the fact the Stop the Boycott campaign despite legal advice which clearly states that any boycott of Israeli academia would be in breach of the unions own anti-discrimination policies and British anti-discrimination laws.
Jeremy Newmark, Joint Head of the Stop the Boycott Campaign said:
"UCU has again demonstrated how out of touch the it is with the vast majority of its membership and with the wider academic community. This motion does nothing to help the Palestinians.
"Trade Unions exist to defend their members in the workplace. Our legal opinion, produced at the request of UCU members, shows that this motion promotes discrimination. It runs counter to all that a Trade Union should stand for, discriminating against some of its members instead of defending all of them. "
Lorna Fitzsimons, Joint Head of the Stop the Boycott campaign said:
"What was true last year remains true today.
"Boycotts of any kind do nothing to promote peace and moderation in the Middle East, as well as undermining the academic freedom and integrity of British academic institutions.
"A boycott has never been the right answer for those looking to genuinely help Palestinians and Israelis. The way forward must be to build bridges, encourage dialogue and allow ordinary Israelis and Palestinians the opportunity to engage with each other.
"This motion in effect gives license to harassment and discrimination within academic institutions - the very thing the UCU is supposed to protect its members from.
"As a trade unionist myself I find it astounding that the Union is prepared to contradict its founding principles of protection in the workplace. Ferocious and free debate is of course vital within all aspects of society - but only if there is no threat attached to individuals."
