Obama quickly sent his congratulations to the mayor-elect. "As a Chicagoan and a friend, I couldn't be prouder," the president said in a statement. "Rahm will be a terrific mayor for all the people of Chicago."
Emanuel's relationship with Obama won him votes from a number of people who believed his White House connections would be an advantage.
Obama political adviser David Axelrod said Chicago would get "whatever the city's entitled to. ... And I don't think Rahm will leave one dollar on the table."
During his time in Congress, Emanuel served as chairman of the Democratic Congressional Campaign Committee and was credited with helping lead Democrats to victory in 2006, when they won the majority in the House after a dozen years in the minority.
The new mayor faces a daunting series of challenges, including fixing the city's dire finances, addressing underfunded employee pensions and confronting a shrinking urban population.
Daley has been criticized for allowing the city to spend beyond its means, and Chicago was not spared the pain of the economic downturn of the last few years.
The city's inspector general's office warned in October that Chicago's annual deficit surpassed $1 billion when combining recent budget deficits with the spending increases the city would need to properly fund its pension system. [Read about the deficit and national debt.]
Emanuel may come under pressure to raise taxes and cut services and public employee benefits, though those measures would be politically difficult.
The new mayor will also have to find new leadership for city schools and a new police superintendent. All the candidates have talked about wanting to replace Jody Weis with someone who has a stronger focus on neighborhood policing.
As recently as January, Emanuel's candidacy was imperiled by a legal challenge to knock him off the ballot over the city's requirement that candidates live in the city for at least one year prior to running.
More than two dozen people challenged Emanuel's eligibility because he had lived in Washington for nearly two years while working for Obama, and he had rented out his Chicago home.
Emanuel moved back to Chicago in October after Daley announced he would not seek a seventh term.
The matter went all the way to the Illinois Supreme Court, which overturned a lower-court ruling that briefly threw Emanuel off the ballot.
But all that turmoil seemed far behind Tuesday as Emanuel paid tribute to his supporters.
"Thank you, Chicago, for this humbling victory. ... You sure know how to make a guy feel at home."