Senate Democrats raised concern about Bolton's allegedly rough treatment of subordinates as well as allegations he tried to distort intelligence reports in his previous post as the administration's top arms-control official.
But Bush used his authority to temporarily appoint Bolton during the U.S. Congress's summer recess. The assignment will last about 18 months.
Presidents rarely use such authority for high-level appointments, but Bush pointed to the importance of the UN for U.S. policy.
"America has now gone more than six months without a permanent ambassador to the United Nations," Bush said. "This post is too important to leave vacant any longer, especially during a war and a vital debate about UN reform."
Bush praised UN cooperation with the United States in areas such as spreading democracy, relieving hunger, and helping victims of disaster. He said this is a time of opportunity for the United States and the United Nations.
"We've helped to lay the groundwork for two landmark events in the history of liberty: the free elections of Afghanistan and Iraq," Bush said. "Ambassador Bolton will work to build on that progress by helping the UN continue to find effective new ways to match its good intentions with good results."
Democrats in the U.S. Senate protested the move, saying it would undermine credibility of the U.S. ambassador at a crucial time.
Asked for his reaction at a news briefing, UN Secretary-General Kofi Annan told reporters Bolton was "very able and very bright." He said he was confident he would be able to work with Bolton.
"I think it is the president's [Bush's] prerogative when the president has decided to appoint [Bolton] through this process for him to come and represent him and, from where I stand, we will work with him as the representative of the president and the government," Annan said.
Bolton has been a long-time critic of the UN. But he said today that he would work "tirelessly" to advance U.S. initiatives and create a more effective UN.
"We seek a stronger, more effective organization, true to the ideals of its founders and agile enough to act in the 21st century," Bolton said. "It will be a distinct privilege to be an advocate for America's values and interests at the UN and, in the words of the UN Charter, to help maintain international peace and security."
The United Nations is in the midst of debate over wide-ranging reforms. Possible changes include an expansion of the UN Security Council, the overhaul of the main UN human rights body and a definition for terrorism.