The statue, which stood for 106 years,
is the second monument to come down after the New Orleans City Council voted to remove the four landmarks in 2015.
After years of heated public debate and legal battles, recent court decisions paved the way
for the city to relocate the four monuments.
Dozens of people -- a crowd opposed to the monument's removal as well as those backing it -- gathered at the Davis statue before the operation began, at times screaming insults and threats at each other. Police separated the sides with barriers.
As the statue was lifted shortly after 5 a.m. (6 a.m. ET), those who wanted it removed cheered and sang the chorus from "Na Na Hey Hey Kiss Him Goodbye."
One person held a sign that read, "Bout Time."
The monument's supporters at that point watched mostly in silence, some holding up Confederate banners.
Earlier, some supporters chanted, "President Davis," and one man saluted the statue.
It wasn't immediately clear how long it would take workers to remove the pedestal.
The city government kept quiet about the timing of the removal, citing what it said were threats that some had made toward contractors who would do the work.
But word about the plans spread Wednesday when the principal of a nearby school told parents in a letter that she'd been told the removal would happen overnight, and that they should know a street would be blocked off in the morning, CNN affiliate WGNO-TV reported
Part of a larger controversy
The New Orleans monuments are part of the larger controversy surrounding Confederate symbols, which some say represent slavery and racial injustice. Supporters say they represent history and heritage. The issue became especially prominent after the 2015 massacre of nine black parishioners in a Charleston, South Carolina, church by a self-described white supremacist.
"These monuments have stood not as historic or educational markers of our legacy of slavery and segregation, but in celebration of it," New Orleans Mayor Mitch Landrieu said in a statement released Thursday morning.
"To literally put the Confederacy on a pedestal in some of our most prominent public places is not only an inaccurate reflection of our past, it is an affront to our present, and a bad prescription for our future. We should not be afraid to confront and reconcile our past."
Jefferson Davis statue dedicated in 1911
The Davis statue stood on top of a roughly 12-foot column and depicted the Confederate president with his right arm outstretched, towering over the street also named after him.
Davis lived in New Orleans after the Civil War and died there in 1889. The statue was dedicated in 1911.
In 2004, the words "slave owner" were painted on the base of the monument.
How they extracted the statue
Police had cordoned off the 6-foot tall bronze statue of Davis with a chain-link fence to keep protesters out.
Workers wore helmets as well as what appeared to be tactical vests and face masks. Cardboard and tape covered contractors' names on equipment involved in the controversial operation -- the same methods used during the first Confederate landmark removal April 24.
About 4 a.m., two workers approached the Davis statue in a work lift and wrapped part of it in green plastic.
They tied the statue's torso with yellow straps, securing it to a crane. One worker dislodged the statue's base from the column, using a long flat tool.
Two more statues scheduled for removal
Last month, the city dismantled the first of its four monuments
scheduled for removal -- an obelisk commemorating the Battle of Liberty Place. The monument marked a deadly fight between members of the Crescent City White League, a group opposed to the city's biracial police force, and state militia after the Civil War.
The remaining two monuments -- those of Confederate generals Robert E. Lee and Pierre Gustave Toutant Beauregard -- also are scheduled for relocation.
Landrieu's office has not revealed when the two remaining statues will come down.
The mayor's office said the city has secured private funding to remove the moments. Landrieu said the statues will be put in storage while the city looks for a suitable place to display them, such as a museum.