Mr Giuliani did not "shrink from the pain"
The editors said they had agreed on Mr Giuliani because of his handling of the aftermath of terrorist attacks on the World Trade Center.
Mr Giuliani said he was humbled by the honour.
The editors of Time said they chose the mayor "for having more faith in us than we had in ourselves, for being brave when required and rude where appropriate and tender without being trite, for not sleeping and not quitting and not shrinking from the pain all around him".
Time staff spent hours debating whether to give the title to Bin Laden, managing editor Jim Kelly said, and the magazine had been widely expected to name him.
The accolade is meant for the person who has had the biggest influence on the news, whether good or bad, and previous winners include Hitler and Stalin.
But the editors decided Bin Laden was "too small a man to get the credit for all that has happened in America in the autumn of 2001".
Mr Giuliani's communications director, Sunny Mindel, said: "The mayor is very humbled and feels this honour is really being given to the people of the city of New York for their courage and bravery during the most horrific attack on the United States."
Within hours of the attacks Mr Giuliani was at the scene, helping to co-ordinate the emergency response.
He told New Yorkers: "We're going to rebuild, and we're going to be stronger than we were before... I want the people of New York to be an example to the rest of the country and the rest of the world that terrorism can't stop us."
Time's online announcement of the award includes an audio account of 11 September, as told by Mr Giuliani and his aides.
Asked how much of his visible confidence had been a bluff, the mayor responded: "Some."
He added: "Look, in a crisis you have to be optimistic. When I said the spirit of the city would be stronger, I didn't know that. I just hoped it. There are parts of you that say, 'Maybe we're not going to get through this.' You don't listen to them."
Before the attacks, the mayor's popularity was reaching an all-time low, with US newspapers full of details about his divorce and accounts of his angry public outbursts.
But his conduct earned him high praise from New Yorkers and national politicians.
Barred from running for a third term, Mr Giuliani leaves office on 31 December when his successor, Michael Bloomberg, is to be sworn in.