Bloomberg first won office as a Republican but split from the party and now runs the biggest US city as an independent. He did not endorse a candidate in 2008, having backed Republican George W. Bush in 2004.
He said the president's reaction in the wake of this week's devastating superstorm, which swamped much of lower Manhattan and killed 37 people in the city, had influenced his decision to endorse the Democrat.
"The devastation that Hurricane Sandy brought to New York City and much of the Northeast -- in lost lives, lost homes and lost business -- brought the stakes of Tuesday's presidential election into sharp relief," he said.
"We need leadership from the White House -- and over the past four years, President Barack Obama has taken major steps to reduce our carbon consumption, including setting higher fuel-efficiency standards for cars and trucks."
The statement was carried as an op-ed on the wires of Bloomberg's eponymous news agency, five days before polling day.
Obama, locked in a tight race with Republican Mitt Romney, quickly welcomed the announcement, saying he was honored by Bloomberg's nod.
"I deeply respect him for his leadership in business, philanthropy and government, and appreciate the extraordinary job he's doing right now, leading New York City through these difficult days," he said in a statement.
Bloomberg's backing was double-edged, noting that while Obama ran as a pragmatic problem-solver and consensus-builder in 2008, he "devoted little time and effort to developing and sustaining a coalition of centrists."
"And rather than uniting the country around a message of shared sacrifice, he engaged in partisan attacks and has embraced a divisive populist agenda focused more on redistributing income than creating it," he added.
Obama admitted the two men had not always seen eye to eye.
"While we may not agree on every issue, Mayor Bloomberg and I agree on the most important issues of our time -- that the key to a strong economy is investing in the skills and education of our people, that immigration reform is essential to an open and dynamic democracy and that climate change is a threat to our children's future," the president said.
There has been a pronounced lack of discussion of climate change on the campaign trail, and the candidates made absolutely no mention of it or of global warming in any of the their three nationally televised debates.
But a heckler made clear mention of it Thursday at a Romney rally.
Moments after the Republican nominee urged voters to keep Hurricane Sandy victims in their hearts and to donate money to relief efforts, a man interrupted Romney, yelling "What about climate?
"That's what caused this monster storm. Climate change!" he shouted, as he held up a banner that read "End Climate Silence," before being escorted out.
Romney stood silent throughout the interruption, while supporters booed the heckler and drowned him out with chants of "USA! USA!"
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Dumb Americans shout USA to everything.
@tutti-frutti: Republican Colin Powell has also endorsed Obama! Mitt was never a general.
Bloomberg is jealous of Mitt. Mitt is almost as rich as he is.
Both Bloomberg and Christie will be needing federal money for disaster relief and Obama is the one will have the signing authority. Good relief work means reelection. You scratch my back and I will yours.