Rockefeller is charged with felony custodial kidnapping, assault and battery and assault and battery with a dangerous weapon.
The exact time of his arraignment has not been set.
He was arrested by FBI agents and Baltimore police, said Special Agent Rich Wolf, from FBI's Baltimore field office.
A "concerned citizen" tipped off authorities that the man known as Clark Rockefeller was living in a Baltimore apartment and had a 26-foot catamaran docked at a nearby marina, Boston Police Commissioner Ed Davis said.
Rockefeller will be arraigned Monday to begin extradition proceedings. He is charged with felony custodial kidnapping, assault and battery and assault and battery with a dangerous weapon, Davis said.
Investigators invented a ruse to get Rockefeller out of the apartment and away from the child. They called the suspect and told him that his boat was taking on water.
He was arrested when he left the apartment, Davis said. The girl, Reigh Boss, was found apparently unharmed inside.
"Her first words were she was very happy to see very nice people ... she was ecstatic," said Noreen Gleason, FBI's assistant special agent in charge of the Boston division.
The girl lives with her mother, Sandra Boss, who works in London as a partner in a global management consulting firm.
Boston Police Department Deputy Superintendent Thomas Lee said that when Boss heard the news that her daughter had been rescued, she collapsed into his arms.
"I caught her. She fainted dead away," Lee said. "She was overjoyed."
Boss is reportedly on her way to reunite with Reigh and has spoken to the girl on the phone, police said.
When the two spoke, Reigh told her mother, "Daddy left me alone but these nice people came to get me," according to Elaine Driscoll, a spokeswoman for the Boston Police Department.
The arrest ended a suspenseful week that began in Boston's Back Bay neighborhood when police said Rockefeller attacked and fled from a social worker during a supervised visit with his daughter.
In what police believe was an elaborate plan, Rockefeller is accused of arranging for two drivers to take them to New York City. He was most recently spotted last Sunday at Grand Central Terminal in New York City.
Police first believed Rockefeller was trying to flee to Bermuda or Peru on a yacht docked on Long Island. But later they found he might have planted false clues to throw investigators off his trail.
Boston police dismissed several witness reports on Friday that the 48-year-old father was spotted in the Caribbean the day before.
Employees at an auto store and at a convenience store said they recognized the high-society man and his daughter Reigh from photos as the people they helped the day before, Turks and Caicos Sgt. Calvin Chase said Friday.
But the sightings were investigated and found not to be credible, Boston Police spokesman Eddy Chrispin said.
Authorities also do not believe Rockefeller sailed to Baltimore because the catamaran has apparently been docked there all along. Elaine Driscoll, a spokeswoman for the Boston Police Department, described the catamaran found in Baltimore as a "real fixer-upper. It would have been tough to get far in it."
Davis said the investigation was ongoing and authorities were still trying to determine Rockefeller's real identity and if anyone else was involved in the abduction.
Rockefeller used at least four known aliases, and there is no indication the fugitive is related to the famous family descended from Standard Oil billionaire John D. Rockefeller Sr., family members said.
Rockefeller allegedly implied to friends and acquaintances that he was a member of the storied Rockefeller clan, as well as allegedly claiming that he was a physicist and a philanthropist.
But as police began investigating him, they found that facts about Rockefeller, who allegedly also went by several other aliases, were hard to come by. Authorities were unable to find a valid social security number or marriage certificate for Rockefeller; one police official described him as a "ghost."
Boston police said investigators have not located a valid Social Security number for Rockefeller. They have also found no wedding certificate documenting his marriage to Sandra Boss, the mother of the missing child who got custody of the little girl after their 2007 divorce, the official said.
The task force has not found any work history for Rockefeller, who told one former neighbor in New Hampshire that he was a "physicist" and fashioned himself as a "philanthropist" who sat on the boards of various nonprofits.
Investigators also are unclear about Rockefeller's education history, the official said, despite reports that he commonly told acquaintances he attended Yale and Harvard. Some people have told authorities that Rockefeller said that his parents died in a car crash when he was young; others were told he was homeschooled as a kid.