Mr Moon told President Xi Jinping that North Korean provocations had to stop before the deployment of the Terminal High Altitude Area Defence (Thaad) system could be reconsidered.
Yoon Young-chan, a spokesman for the South Korean administration, said the call had explained China's position over the deployment of THAAD to Mr Moon, who took office on Wednesday.
Despite Chinese anger at North Korea's repeated nuclear and missile tests, China remains the isolated state's most important economic and diplomatic backer, even as Beijing has signed up for tough United Nations sanctions against Pyongyang.
President Moon Jae-in told his Chinese counterpart Xi Jinping that he's aware of Beijing's concerns over a US missile shield installed on South Korean territory and will work to resolve the problem.
He will send a delegation to Beijing to discuss both North Korea and Thaad.
During his first speech as president, Moon said he would aim to sooth tensions between Beijing and Washington. Moon accepted Trump's invitation to visit at an "early date".
After all, it was during the liberal Roh presidency that South Korea concluded the South Korea-US Free Trade Agreement, allowed for US troops to be redeployed within its borders and dispatched its own troops to fight alongside the US in Iraq.
"For a long time, China has upheld the goal of the denuclearization of the Korean Peninsula, protecting the peace and stability of the peninsula and resolving the problem via dialogue and consultation", Xi said.
US admiral: North Korea's actions 'recipe for disaster'
He said the council is exploring many different avenues to proceed and "clearly sanctions are a way to go", but also diplomacy. The Indian-American said any country that doesn't implement United Nations sanctions is supporting Pyongyang's actions.
Tensions in Korean Peninsula escalated in recent months after Pyongyang conducted a number of nuclear tests and ballistic missile launches.
The protest was lodged by the recently revived Foreign Affairs Committee of North Korea's Supreme People's Assembly, which said the US House of Representatives was "obsessed" with a sense of disapproval and warned it of dire consequences.
Katherine Moon is a Korea expert with the Center for East Asia Policy Studies at the Brookings Institution in Washington, D.C. She said a policy of engagement might help North Korea, but hurt efforts by the US and allies in East Asia.
"Sanctions against North Korea are also a means to bring the North to the negotiating table aimed at eliminating its nuclear weapons", Yoon told a briefing, adding that Xi indicated his agreement.
South Korean President Moon Jae-in holds a telephone conversation with Australian Prime Minister Malcolm Turnbull at his presidential office in Seoul on May 12, 2017.
They came as North Korea's ambassador to the United Kingdom told Sky News his country will go ahead with its sixth nuclear test at a time and place of its leader's choosing.
He has taken a more conciliatory line with North Korea than his conservative predecessors and advocates engagement.
Asked in an interview with NBC News conducted on Thursday whether Moon's approach would mean a change in USA strategy, Trump replied: "He's more open to discussion". "It remains a concern that the left of centre, left-wing party in South Korea is going to do well", an unnamed US official told the South China Morning Post before Moon's election was confirmed.