He turned up in a government vehicle at a hotel held by loyalists, a day after the rebels said they had detained him.
A BBC correspondent said Saif al-Islam seemed confident and full of adrenalin.
On Monday the rebels met strong resistance from pro-Gaddafi forces as they continued their push. Both sides say they control most of Tripoli.
Saif al-Islam Gaddafi turned up at Hotel Rixos in the early hours of Tuesday.
He told the BBC's Matthew Price: "We have broken the backbone of the rebels." He added that by moving into Tripoli, the rebels had fallen into "a trap".
"We gave them a hard time, so we're winning," he said.
Saif al-Islam Gaddafi, 39, had been widely regarded as a likely successor to his father. On Sunday the rebels claimed they had captured him, along with other members of his family.
Asked if Col Gaddafi was safe and in Tripoli, Saif al-Islam replied: "Of course."
The Libyan leader's whereabouts are still unclear. His sprawling Bab al-Azizia compound is being defended by loyalist troops
A diplomatic source told AFP news agency that Col Gaddafi could still be there. He has not been seen in public for months, although he has broadcast audio messages from undisclosed locations.
In a broadcast late on Sunday, he urged residents to "save Tripoli" from the rebels.
In other developments:
Pro-Gaddafi forces fire a suspected Scud missile from near their stronghold city of Sirte, US defence officials tell Reuters news agency
Col Gaddafi's eldest son Muhammad reportedly escaped from rebel custody hours after being detained
China and Russia issue statements urging Gaddafi forces to stop fighting
UN Secretary General Ban Ki-moon says leaders of regional blocs will meet in New York later this week
Egypt formally recognises the rebel National Transitional Council as the legitimate representative of the Libyan people
Ambush
The rebels swept into Tripoli from several direction following an uprising in the capital at the weekend. They who were greeted by jubilant crowds in central Green Square when they arrived on Sunday.
Rebel fighters have set up checkpoints in parts of the city, and say reinforcements are arriving by boat. But they have met stiff resistance in a number of areas.
There was sustained gunfire near the Bab al-Azizia compound in western Tripoli throughout Monday.
Gaddafi loyalists also remain in control of the area further south around the Rixos Hotel, where many Western journalists are based.
A rebel convoy coming in from the west was ambushed by Gaddafi loyalists using anti-aircraft fire on Monday. The convoy forced to pull out of the city.
As night fell the fighting appeared to die down in many areas. Both sides insist they have the upper hand.
Government spokesman Moussa Ibrahim claimed late pro-Gaddafi had control of at least 75% of the city, while the rebels said they were holding about 80%.
Our correspondents says it is impossible to determine who is telling the truth.
World leaders have urged Col Gaddafi to step down. US President Barack Obama said elements of the Gaddafi regime continued to pose a threat.
"But this much is clear: the Gaddafi regime is coming to an end and the future of Libya is in the hands of its people," he said.
He appealed to Col Gaddafi to reduce further bloodshed by "explicitly relinquishing power to the people of Libya and calling on those forces that continue to fight to lay down their arms".