On Friday, the base on a plain near the city of Mazar-e Sharif became the target of the deadliest single attack by Taliban insurgents since their regime in Kabul was overthrown in 2001.
It was not immediately clear who would replace Defense Minister Abdullah Habibi and Army Chief of Staff Qadam Shah Shahim.
Earlier, the defence ministry gave a figure of at least 100 soldiers killed or wounded.
"One facebook user, Abdulahi, said on facebook: "(President Ashraf) Ghani also needs to resign". A spokesman for the Islamist militia claimed responsibility for the assault.
The exact toll from Friday's assault in the northern province of Balkh remained unclear, with some local officials putting the number of dead alone as high as 130.
The departures came as Pentagon chief Jim Mattis arrived unannounced in Kabul to access the continuing need for United States troops in the lengthy war.
General Daulat Waziri said there were 10 attackers, including the two who carried out the suicide attacks.
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Ghani on Saturday traveled to the base in Balkh from where he strongly condemned the attack, according to a tweet from the official Twitter account of the presidential palace.
The German military, which has led much of the advising effort in northern Afghanistan, said in the wake of the attack it would continue to work with the Afghans.
Mattis is in Kabul to assess America's longest war as the Trump administration weighs sending more USA troops.
Almost 9,000 U.S. troops remain in Afghanistan, in addition to thousands of global coalition forces.
An Afghan national Army stands guard at a checkpoint in the Kabul-Jalalabad highway on the outskirts of Kabul, Afghanistan, Saturday, April 22, 2017.
The five-hour assault, the deadliest ever by the group on a military base, underscores its growing strength more than 15 years after it was ousted from power.
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