The appointment came after the opposition-led parliament failed to issue a report on the outcome of its confirmation hearing for the new top diplomat, Kang Kyung-wha.
Moon earlier stressed a need to have a foreign minister before his summit with U.S. President Donald Trump later this month, as well as the Group of 20 summit in Germany in early July.
Initially, the parliament had until Wednesday to publish a report on Kang's confirmation hearing held June 7.
Moon gave the parliament an additional period after the initial deadline expired.
The president is required by law to offer a second chance of up to 10 days for the parliament to publish a report on a confirmation hearing.
Moon had offered an additional three days, The second deadline expired Saturday.
The president does not need parliamentary approval to appoint new ministers. However, his appointment of Kang is widely expected to put strains on his already shaky ties with the opposition-led parliament.
The main opposition Liberty Korea Party earlier threatened to boycott the ongoing parliamentary session should the president appoint the new foreign minister without its blessing.
Such a boycott, if it takes place, may effectively prevent appointments of at least 10 minister designates waiting to be reviewed and confirmed by the National Assembly.
It may also cripple government efforts to secure an 11.2 trillion-won (US$10 billion) extra budget that is designed to boost the local economy and also create up to 110,000 new jobs in the public sector.
The main opposition party controls 107 seats in the 300-seat National Assembly. The ruling Democratic Party controls 120 seats, the largest number of seats held by any single party in the unicameral parliament but still far short of a house majority.
Kang, a former UN official, was accused of various past wrongdoings, including alleged tax evasion and false registration of address for her daughter, which is a crime punishable by a jail term of up to three years or a maximum fine of 10 million won.
More importantly, they are part of five corruptive crimes the president had once said should keep their violators away from any high government offices.
Following the controversy over past wrongdoings of Kang and other minister designates, the president insisted his nominees must be evaluated for their abilities and their past wrongdoings in the context of when and why they were committed.
"Kang is a confident and great woman," he said earlier. "She has been recognized and praised for her abilities as a diplomat in the United Nations and the international community. As they say, she is a global figure. I believe it is about time we had such a global figure as our foreign minister."