They bundled the screaming boy into a vehicle and drove him away in an unmarked car under cover of darkness, as people outside the house shouted protests.
A swat team of about 25 officers broke down the door of the home of the boy's uncle, Lazaro Gonzalez, and re-emerged seconds later with the boy wrapped in a blanket.
They bundled the screaming boy into a vehicle and drove him away in an unmarked car under cover of darkness, as people outside the house shouted protests.
Chaotic scenes followed outside the house as the officers retreated. Pepper spray was used to keep back the crowd.
Elian was put on a plane and flown to at Andrews Air force base outside Washington where he was reunited with his father for the first time in five months.
Donato Dalrymple, one of the fisherman who rescued Elian last year, was in the home at the time of the snatch.
He said federal agents pointed guns at the family and shouted: "Give me the boy or I'll shoot you!"
As they left, the officers are reported to have shouted "Bingo! Bingo!" as a signal that they had the boy.
In a brief statement, President Bill Clinton said that he supported Attorney-General Janet Reno's decision to order the raid after negotiations with the Miami relatives failed.
"The law was upheld and that was the right thing to do," he said.
Speaking to the press, Ms Reno gave the assurance that Elian would remain in the US in accordance with the appeal court injunction against the boy's being taken to Cuba.
"We have been to great lengths to resolve this in the least disruptive way possible. Up until the last moment we tried every way we could to encourage Lazaro Gonzalez to voluntarily hand over the child.
"Unfortunately the Miami relatives rejected our efforts leaving us no option but the enforcement action," Ms Reno said.
Ms Reno defended the use of armed officers. She said that despite pictures of an armed officer next to a distraught Elian, the automatic rifle had not been pointed at the boy and the officer's finger was not on the trigger of the gun.
She said her department had had information that there might have been guns in the house and in the crowd outside.
The move to seize Elian came after the apparent failure of late-night negotiations on a compromise solution that might have allowed some form of joint custody between Elian's Miami family and his father, Juan Miguel Gonzalez.
Anger
In Miami, there were angry scenes as Cuban exiles threw stones at federal officers.
Donato Dalrymple said: "They took this kid like a hostage in the night time. They should let him come out with dignity."
A man in the crowd promised civil disobedience. "We're going to close Miami," he said.
Some protesters tore up US flags. Other members of the Cuban exile community tried to stop them.
The mayor of Miami, Joe Carollo, described the federal action as shameful and unnecessary.
Our correspondent reports that Cuban leaders believe the operation will have caused Elian everlasting emotional damage.