Nato's International Security Assistance Force (ISAF) has already been operating in western and northern Afghanistan and in the capital, Kabul.
But Monday's transfer of power from the US-led coalition brings about 8,000 British, Canadian, Dutch and US troops under ISAF command in six volatile southern provinces.
ISAF commander, British Lieutenant-General David Richards, said in a statement: "Nato is here for the long-term, for as long as the government and people of Afghanistan require our assistance."
The south, the Taliban's heartland from where the movement rose to take control of most of the goverment by 1996, sees the worst of the insurgency with regular suicide and roadside bombings, most of them directed at troops.
Military officials also admit that the insurgents are better organised than ever, able to launch attacks on coalition bases.
The takeover also coincides with a surge in fighting in Afghanistan since the Taliban was toppled that has left hundreds of people dead.
The force is hopeful however it can make a difference with a stronger emphasis on rebuilding, while the coalition maintains a force focused on counterinsurgency work.
"That doesn't mean we will not fight," Richards said.
But he hoped that "the people's own desire to defend what they see developing in front of them ... will enable us to achieve success" over a "reasonable" period of time.
ISAF said in a statement the force intended to continue coalition efforts to "provide security as well as reconstruction projects and humanitarian assistance".
In July the US said it hoped to cut its force levels in Afghanistan from 19,000 to 16,000 in 2006, but instead had been adding more troops as the Taliban mounted its largest spring offensive since the war in 2001.
On Saturday coalition and Afghan troops killed 20 fighters in the southern Uruzgan province, while another six were killed on Sunday by Afghan forces in the southeast.
Four fighters also died in separate explosions while planting bombs in the southern Kandahar province.
Suspected Taliban militants also fired a rocket at an Afghan girls' school in Kandahar city on Sunday, wounding one student.