Aoun, who spoke at the start of his talks with Russian President Vladimir Putin in the Kremlin, said Trump's decision "undermines the foundations and rules of the United Nations and international law" and "causes particular concern in the countries neighboring Israel."
Trump's move made the U.S. the first country to recognize Israel's sovereignty over the Golan, which was captured from Syria in the 1967 Mideast war and regarded by the rest of the international community as occupied territory.
Russian officials and lawmakers have criticized Trump's decision as destabilizing, but Putin refrained from commenting on the issue during his opening remarks at the start of the talks. The Russian leader hailed Lebanon as Moscow's "traditional partner" in the region.
Aoun, who arrived in Moscow on Monday, focused on efforts to encourage the return of Syrian refugees. Lebanon has taken in over 1 million refugees from neighboring Syria, which is equivalent of a quarter of Lebanon's population.
Lebanese politicians are divided over how to handle relations with the Syrian government and repatriation of refugees and look to Moscow to help to mediate that. At a meeting with Russian lawmakers earlier Tuesday, Aoun said that Lebanon faces "a terrible economic fallout" from the Syrian crisis and expressed hope that Russia would help his country repatriate the Syrians.
Russia, which has waged a military campaign in Syria that helped President Bashar Assad's government reclaim wide swaths of territory, has strongly pushed for the refugees' return and criticized the West for failing to offer support.
In a joint statement issued after the Kremlin talks, Russia and Lebanon called on the international community to help create favorable socio-economic conditions for the refugees' return by helping Syria's post-war reconstruction.
Nataliya Vasilyeva contributed to this report.