Crowds across the country fired guns and hooted car horns to celebrate the seizure of the British-educated 39-year-old, who a year ago appeared a possible successor to rule the oil-producing desert state.
Hundreds of people crowded round the plane carrying him after it landed in Zintan, trapping him inside and raising fears he might suffer a similar fate to his father, who was beaten and shot after his capture a month ago on Sunday.
Saif al-Islam was later taken away uninjured and Prime Minister-designate Abdurrahim El-Keib promised that Gaddafi's son would face a fair trial.
"We assure Libyans and the world that Saif al-Islam will receive a fair trial ... under fair legal processes which our own people had been deprived of for the last 40 years," Keib told a press conference in Zintan.
Saif al-Islam, who had vowed to die fighting but was taken without a struggle, was arrested overnight, officials said.
"At the beginning he was very scared. He thought we would kill him," Ahmed Ammar, one of his captors, told Reuters.
Saif al-Islam told a Reuters reporter on his plane he had wounded his hand during a NATO air strike a month ago. Asked if he was feeling all right, Gaddafi said simply: "Yes."
The Zintan fighters, who make up one of Libya's most powerful militia factions that hold effective power in a country still without a government, said they planned to keep him in Zintan until they could hand him over to the authorities.
Keib is scheduled to form a government by Tuesday, and the fate of Saif al-Islam will be an early test of its authority.
The incoming premier said Gaddafi's son remained in the hands of "the revolutionaries in Zintan" and heaped praise on their fighters, acknowledging the authority the tribal militia continued to hold over its territory.
"They (the Zintan fighters) will keep him in peace, take care of him. He will be treated as any human being with respect. He will get his day in court," El-Keib said. He said the detention was the "crowning" of the uprising that overthrew Muammar Gaddafi.
Libyans want to try Saif al-Islam at home and believe he knows the location of billions of dollars of public money amassed by the Gaddafi family. His captors said they found only a few thousand dollars and a cache of rifles in seized vehicles.
The European Union urged Libyan authorities to ensure Saif al-Islam was brought to justice in cooperation with the International Criminal Court, which accuses him of crimes against humanity.
Ammar told Reuters that his unit of 15 men in three vehicles, acting on a tip-off about a possible high-profile fugitive, had intercepted two cars carrying Gaddafi and four others in the desert about 70 km from the small oil town of Obari at about 1:30am.
After the fighters fired in the air and ground to halt the cars, they asked the identity of the passengers. The man in charge replied that he was "Abdelsalam" - a name that means 'servant of peace'. But the fighters quickly recognised Saif al-Islam and seized him without a fight.
The fighters said they put him at ease and he accepted he would be taken to Zintan, a town in the western mountains south of Tripoli that was a stronghold of anti-Gaddafi rebels.
Saif al-Islam appeared relatively at ease and was not handcuffed as he sat on a bench at the rear of the plane.
Wearing traditional robes with a scarf pulled over his face, Saif al-Islam had a heavy black beard and wore his rimless spectacles.
His thumb, index and another finger were heavily bandaged from the wounds sustained in the NATO strike.
Muammar Gaddafi's beating, abuse and ultimate death in the custody of former rebel fighters was an embarrassment to the previous transitional government. Officials in Tripoli said they were determined to handle his son's case with more order.
"The capture presents a challenge to the NTC. If they want to try Saif then what can they do to make Zintan hand him over?" said Henry Smith, an analyst with the Control Risks group, referring to the National Transitional Council which won international recognition as Libya's new interim government.
"They may leave his fate to Zintanis but then where does that leave Libya's embryonic judicial system? This is an acid test of the NTC's authority."
Memories are still fresh of the days Gaddafi's father's corpse spent rotting and on public view in the city of Misrata, another rebel stronghold, as its militia leaders trumpeted their capture of the fallen leader as part of their campaign to extract power and patronage from the new interim authority.
A fighter from an anti-Gaddafi unit, the Khaled bin al-Waleed Brigade, which said it seized Saif al-Islam in the wilderness near the oil town of Obari, told Free Libya television: "We got a tip he had been staying there for the last month.
"They couldn't get away because we had a good plan," Wisam Dughaly added, saying Saif al-Islam had been using a 4x4 vehicle: "He was not hurt and will be taken safely for trial so Libyans will be able to prosecute him and get back their money.
"We will take him to Zintan for safekeeping to keep him alive until a government is formed and then we will hand him over as soon as possible," Dughaly said.
He added that Saif al-Islam, once seen as a reformer who engineered his father's rapprochement with the West, appeared to have been hiding out in the desert since fleeing the tribal bastion of Bani Walid, near Tripoli, in October.
"I'm really surprised that Saif al-Islam has not met the same fate as his father and his brother," Fawaz Gerges, professor of international relations at the London School of Economics, told BBC TV.
"The best thing that the new leadership can do is to hand Saif al-Islam to the International Criminal Court because I don't believe it really has the resources and the means to try Saif al-Islam and give him a fair trial."
Asked of the chances of that, he said "Almost zero." He said he expected him to get the death penalty and be executed in Libya. "This is unfortunate for the new Libya," he said.
The ICC only acts if a country is unable or unwilling to investigate or prosecute a suspect, for instance when its legal system has collapsed.
Justice Minister Alagy said he was in touch with the ICC over how to deal with Gaddafi.
"We Libyans do not oppose the presence of international monitors to monitor the trial procedures that will take place for the symbols of the former regime," he told Al Jazeera.
Other Libyan officials have said a trial in Libya should first address killings, repression and theft of public funds over the four decades of the elder Gaddafi's personal rule.
There was no word of the other official wanted by the ICC, former intelligence chief Abdullah al-Senussi.
The ICC said on Saturday it had received confirmation of the arrest of Saif al-Islam from Libya's Ministry of Justice.
"We trust that the Libyan authorities and the International Criminal Court will ensure that justice runs its course, so that the new Libya can be built on the rule of law and respect for human rights," NATO spokeswoman Oana Lungescu said.
In June, the ICC issued arrest warrants for Muammar Gaddafi, Saif al-Islam and al-Senussi on charges of crimes against humanity after the U.N. Security Council referred the Libyan crisis to the court in February.
