The French leader's whirlwind tour came as troops worked to secure Kidal, the last bastion of radicals who seized control last year after a coup, raising fears that an area larger than France could become a safe haven for al Qaeda-linked fighters.
Welcoming Hollande, thousands of people gathered in the central square of the fabled city of Timbuktu, dancing to the beat of drums -- a forbidden activity during the extremists' 10-month occupation.
Hollande told the crowd France's mission was not finished yet but that African countries would soon have to take over.
"We've already done a lot of work. It's not over yet, it's going to take several weeks, but our goal is to pass the baton," he said.
"We have no intention to stay. Our African friends will be able to do the job we've been doing until now."
Mali's interim president Dioncounda Traore, who joined hands with Hollande and raised them in a victory salute, thanked his counterpart for the "efficiency" of the French troops, which he said had allowed the north to be freed from "barbarity and obscurantism".
Hollande and Traore, who met in the central garrison town of Sevare before travelling to Timbuktu, visited the city's 700-year-old mud mosque of Djingareyber and the Ahmed Baba library for ancient manuscripts, both targeted by destructive Islamist militants.
"There's a real desire to annihilate. There's nothing left," Hollande told the mosque's imam as they visited two ancient saints' tombs that the extremists attacked with pickaxes in July, considering them heretical.
"We're going to rebuild them, Mr President," said Irina Bokova, the head of UNESCO, which is trying to assess the scale of the damage to Mali's ancient heritage.
Timbuktu, a caravan town at the edge of the Sahara that rose to fame in the 14th century as a gold and salt trading hub, was under tight security, with French troops stationed every 100 metres (yards).
Hollande, whose surprise decision to intervene in Mali three weeks ago made him a hero in the former French colony, was greeted with cheers of "Long live France! Long live Hollande!"
"The women of Timbuktu will thank Francois Hollande forever," said 53-year-old Fanta Diarra Toure.
"We must tell him that he has cut down the tree but still has to tear up its roots."
Reprisal attacks With the rebels ousted from all major towns but Kidal, France is keen to hand over to nearly 8,000 African troops slowly being deployed and which the United Nations is considering turning into a formal UN peacekeeping force.
But there are warnings that Mali will need long-term help and fears that the Islamists will now wage a guerrilla campaign from the sparsely populated north.
The joy of citizens throwing off the yoke of brutal Islamist rule, under which they were denied music and television and threatened with whipping, dismemberment and execution, has been accompanied by a grim backlash against light-skinned citizens seen as supporters of the extremists.
Rights groups have reported summary executions by both the Malian army and the Islamists.
Human Rights Watch said Friday that Islamists had killed at least seven Malian soldiers by slitting their throats or shooting them in the mouth, and that Malian troops had shot at least 13 suspected Islamist supporters in Sevare and dumped them into wells.
The Malian army has denied any crimes by its forces.
Amnesty International also called on the French army to launch an investigation into the deaths of five civilians killed in a helicopter attack on the town of Konna at the start of the campaign.
France said it had no helicopters active in the town at the time.
Mali's military was routed at the hands of rebel groups in the north, whose members are mostly light-skinned Tuaregs and Arabs, before the French army came to its aid.
With fears of reprisal attacks high, many Arabs and Tuaregs have fled.
A record number of refugees -- some 1,300 a day -- have been fleeing to neighbouring Mauritania, officials there said.
In all, the crisis has caused some 377,000 people to flee their homes, including 150,000 who have sought refuge across Mali's borders, according to the UN.
The French-led campaign has met little resistance, with many of the Islamists believed to have slipped into the desert hills around Kidal.
While largely supported by the French public, the intervention has not yet paid domestic political dividends for Hollande, failing to reverse a steep slide in his approval ratings as the economy struggles.
After Timbuktu, Hollande and Traore were due to fly to Bamako for a working lunch.