Speaking to reporters in the Oval office, George Bush, the US president, said that he had accepted Bolton's resignation reluctantly.
He said: "I'm not happy about it."
Bush bypassed the Senate and appointed Bolton to the UN job on a temporary basis in August 2005 despite protests that he would pursue a unilateral foreign policy.
Bolton had a history of angering diplomats and colleagues in his previous state department job and his nomination has languished in the Senate Foreign Relations Committee for more than a year, blocked by Democrats and several Republicans.
The Democratic takeover of the Senate in elections in November made the path even more difficult.
Bush said in the presence of Bolton and his wife: "I think he deserved to be confirmed. And the reason why I think he deserved to be confirmed is because I know he did a fabulous job for the country."
Juergen Trittin, a former environment minister and deputy head of the opposition Greens in the German parliament, said: "The bull is leaving the china shop of multilateral politics. This is good news for the world and the US."
The White House re-submitted
Democratic Senator Joe Biden, the incoming chairman of the Senate Foreign Relations Committee, said he saw "no point in considering Mr Bolton's nomination again".
While Bush could not give
Appreciation
As late as last month, Bush, through his senior aides, said he would not relent in his defence of Bolton, despite opposition from Democrats who view
Perino said that among Bolton's accomplishments, he assembled coalitions addressing
She said he also made reform at the United Nations a priority because the
"Despite the support of a strong bipartisan majority of senators, Ambassdor Bolton's confirmation was blocked by a Democratic filibuster, and this is a clear example of the breakdown in the senate confirmation process," she said.
"Nominees deserve the opportunity for a clean up or down vote. Ambassador Bolton was never given that opportunity."
Perino said Bush had reluctantly accepted
