At the peak of the invasion, more than 10,000 soldiers controlled 137 bases. Only 4,000 troops currently remain in the country.
The last of the equipment was brought back from of one of the biggest bases on Saturday.
British forces are due to end their combat role at the end of the year. The country has lost 448 soldiers in Afghanistan since the first casualty in 2002.
In a complex and well-planned operation spanning more than a month, Main Operating Base (MOB) Lashkar Gah and Patrol Base (PB) Lashkar Gah Durai have been handed over to Afghan control. A third base, MOB Price, has also been closed.
From a peak of 137 UK bases, just Camp Bastion, which remains the main base for UK personnel and Observation Post Sterga 2 are now under UK control.
Officials confirmed that the majority of the former UK bases are now in the hands of the Afghan National Security Forces (ANSF).
Afghan forces are now leading 97% of all security operations across the country and are carrying out over 90% of their own training.
Defence Secretary Philip Hammond said on Monday "The handover and closure of our bases across Helmand underlines the progress UK forces have made to increase security and stability across the province but also to build up the capability of the Afghan forces who will carry that work forward".
Hammond added "UK combat operations will cease by the end of this year but our support for the Afghan people will continue. Meanwhile, our troops will continue the mammoth task of getting our people and equipment home by Christmas".
MOB Lashkar Gah was handed over to the Afghans on 24 February 2014 during a ceremony attended by civilian and military leaders from the district centre. It opened in 2006 and served as the headquarters of UK military forces in Afghanistan until August 2013 when Task Force Helmand moved to Camp Bastion. Patrol Base Lashkar Gah Durai, handed over to the Afghans on March 8, 2014, commands an important junction in Helmand.
MOB Price, which has been closed, was formerly home to Danish armed forces and was the UK's largest forward location for most of Operation Herrick.