Fighting lasted for several hours near the city of Mazar-e Sharif in northern Balkh province.
Insurgents targeted those leaving Friday prayers at the base's mosque and others in a canteen, the army said.
The Taliban said in a statement they had carried out the attack, using suicide bombers to breach defences.
Earlier estimates put the death toll as high as 134, but a statement from the defence ministry on Saturday gave the figure of more than 100 killed or injured.
It is one of the deadliest tolls in a Taliban attack on the Afghan army.
At least 10 Taliban militants were also killed in the fighting and one attacker was detained.
The Afghan government has declared Sunday a day of national mourning.
Separately, the US military command in Afghanistan said that Taliban commander Quari Tayib had been killed in a coalition air strike.
It said that Tayib was "once known as the shadow Taliban governor of Takhar province" in the north-east, and was killed along with eight other Taliban fighters in the strike on 17 April.
The Taliban fighters who attacked the base wore army uniforms and drove through checkpoints to launch the raid, a military spokesman said.
One injured soldier, Mohammad Hussain, said: "When I came out of the mosque, three people with army uniforms and an army vehicle started shooting at us. Of course, they had some infiltrators inside the base, otherwise they would never have been able to enter.
"One of them sitting inside a vehicle had set up a machine gun at the car's window and shot everyone in his way."
President Ashraf Ghani flew to the area on Saturday and visited wounded troops.
US military spokesman John Thomas described the attack as a "significant" strike, but he praised Afghan commandos for bringing the "atrocity to an end".
There are conflicting reports about casualties. The defence ministry confirmed more than 100 soldiers had been "killed or injured" but a security official in Mazar-e Sharif told the BBC that more than 100 had died, including a top military commander.
Relatives of some of the soldiers gathered outside the base to take possession of coffins. They all questioned the security measures in place at the main entrance.
"If strict inspections had taken place, the attackers would not have passed the first gate," said Jan Agah, from Jowzjan province. One of his nephews serving at the base died and another was injured in the attack.
The raid shows the Taliban can plan and carry out complex attacks. The militants said four of the attackers had served as soldiers for a long time and had knowledge of every corner of the base.
The base at Mazar-e-Sharif is home to the Afghan National Army's 209th Corps, responsible for providing security to most of northern Afghanistan, including Kunduz province - which has seen heavy recent fighting.
Several German and other foreign soldiers are reported to be garrisoned there.
Last month about 50 people were reported to have died when militants believed to be from the group known as Islamic State targeted patients and staff at a military hospital in Kabul with guns, grenades and knives.
Also in March the Taliban said they had captured the crucial south Afghan district of Sangin after a year-long battle.
More than 100 Afghan soldiers were killed or wounded in a Taliban attack on an army base on Friday, the defence ministry has confirmed.