Saif was captured in the town of Obari along with two aides who were trying to smuggle him out to neighbouring Niger, Libyan militia commander Bashir al Tayeleb said.
Thunderous celebratory gunfire shook the Libyan capital Tripoli as the news spread.
He was the last of Gaddafi's sons to be accounted for.
An ICC prosecution office spokeswoman said: "We are co-ordinating with the Libyan Ministry of Justice to ensure that any solution with regards to the arrest of Saif al Islam is in accordance with the law."
An ICC prosecutor will travel to Libya soon for talks on where Saif will be tried.
The 39-year-old, who studied in the UK, is wanted for crimes against humanity.
Soon after his arrest, a photograph was circulated by the Free Libya group showing Saif with his fingers wrapped in bandages.
The injury was sustained in an air strike a month ago, Saif has said.
Ahmed Ammar, one of the captors, said they acted on a tip off and discovered a vehicle carrying Saif and four others 40 miles from the small oil town of Obari at about 1.30am (local time).
After the fighters fired in the air and ground in order to halt the cars, they asked the identity of the travellers.
They quickly recognised Saif and seized him without a fight.
"At the beginning he was very scared," said Mr Ammar. "He thought we would kill him."
Saif was taken by plane to the city of Zintan, the home of one of the largest revolutionary brigades in Libya.
An angry crowd of hundreds awaited the plane's arrival, preventing his captors from removing the prisoner for an hour. Some people tried to board the plane but were held back.
Anes el Sharif from the Tripoli military council told Sky News that efforts will be made to ensure Saif is treated fairly in custody.
"We don't want what happened [to Colonel Gaddafi] to be repeated again.
"This time we have to show that we are going to treat him well, despite what he has committed to the Libyan people."
Reporters in Tripoli were told Saif would be held in Zintan until there was a government to hand him over to.
The government is due to be formed within days.
"The rebels of Zintan announce that Saif al Islam Gaddafi has been arrested along with three of his aides today," Tayeleb said in an announcement broadcast on Libyan television.
"We hope at this historical moment that the future of Libya will be bright."
There was still no information about wanted former intelligence director Abdullah Senoussi or where he is located.
An arrest warrant for Saif had been issued by the ICC since June 27.
His capture follows the death of his father who was killed a month ago after being captured in his hometown of Sirte.
Before the downfall of the Gaddafi regime, Saif was considered to be the presumptive heir.
The UK Foreign Office told Sky News that they are watching reports closely.
Commentators say Libya is under pressure to handle the detention of Saif in a "civilized" way in the wake of Colonel Gaddafi's bloody death at the hands of rebels.
Former Lib Dem leader Sir Menzies Campbell said: "The government of Libya is on trial. Anything other than due process should not be tolerated.
"The UK did not commit in Libya to tolerate extra-judicial assassination as happened with his father.
"If Libya wishes to take its place among civilised nations it must take this opportunity to demonstrate it's commitment to the rule of law."
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