"The United States urges governments around the world to take appropriate steps to ensure that their funds are not provided directly or indirectly to organizations engaged in anti-Semitic BDS activities", Pompeo's statement concluded.
Pompeo also became the first secretary of state to tour the Golan Heights, whose annexation by Israel from Syria was recognised by Trump.
The resolution emphasized "the right of the Palestinian people to self-determination, including the right to their independent State of Palestine" and "stressed the urgency of achieving without delay an end to the Israeli occupation that began in 1967 and a just, lasting and comprehensive peace settlement between the Palestinian and Israeli sides", based on a two-state solution.
"We will immediately take steps to identify organisations that engage in hateful BDS conduct and withdraw U.S. government support for such groups", he said after meeting Israeli Prime Minister Benjamin Netanyahu.
"We want to stand with all other nations that recognise the BDS movement for the cancer that it is". However, Israel sees the movement as a threat to its state that seeks to strategically damage its security and economy.
Activists strongly deny the charge, comparing it to the economic isolation that helped bring down apartheid in South Africa.
Pompeo held no meetings with Palestinians, who protested his actions and dismissed them as the latest sign of the outgoing Trump administration's strong bias against them.
Pompeo met with Netanyahu and then travelled to the West Bank to visit a settler winery, which has a blend named after him.
On the way there, he made a stop at Qasr el Yahud, revered as the site of the baptism of Jesus in the Jordan Valley, according to the same official. The two governments have shared close ties throughout the years.
But Palestinians and much of the world regard those settlements as illegal under worldwide law. Pompeo said on Thursday that the recognition was "historically important and simply a recognition of the reality".
"Canada's vote today is a reflection of our longstanding commitment to the right of self-determination for both Palestinians and Israelis", said Canada's UN Ambassador Bob Rae in his explanation of the vote to the General Assembly.
The decision on labelling "blatantly violates worldwide law", said Nabil Abu Rudeinah, a spokesman for Palestinian President Mahmud Abbas, dismissing it as another biased move by Mr Trump's administration. "The United States is, therefore, committed to countering the Global BDS Campaign as a manifestation of anti-Semitism".
Pompeo warned the Islamic republic in comments Wednesday that the deals the UAE and Bahrain have reached with Israel showed "its influence in the region is waning".