Malong was sacked via a presidential decree that was announced on Tuesday on national television by Kiir himself.
General James Ajongo Mawut, the former deputy chief of general staff for administration and finance, was named new head of armed forces.
South Sudan descended into conflict in December 2013 after Kiir accused his former deputy Riek Machar, who he had sacked earlier that year, of plotting a coup.
The clashes that followed set off a cycle of retaliatory killings that have split the world’s newest country, which won its independence from Sudan in 2011, along ethnic lines.
As Kiir – from the Dinka ethnic group – fought it out with rebels allied to Machar – a Nuer – both sides committed atrocities, including massacres and gang rape, according to the UN and the African Union.
In February, several senior army officers resigned, accusing Malong of conducting anethnic war against non-Dinkas and ruling with an “unqualified clique of friends and relatives”.
Among those who quit was Lieutenant-General Thomas Cirillo who has since announced plans to launch his own rebellion.
Malong is widely regarded by some as being the mastermind of fighting that erupted in the capital, Juba, last July, killing hundreds and dashing hopes of a power-sharing government between Kiir and Machar
Foreign diplomats repeatedly accused him of undermining the country’s 2015 peace agreement.
The conflict has triggered famine in parts of the country, forced millions from their homes and killed tens of thousands so far.
Separately, gunmen attacked the vice president’s convoy on Tuesday and wounded three of his bodyguards, a government official told the Reuters news agency.
First Vice President Taban Deng Gai, who joined the government after defecting from the main rebel group last year, was not in the convoy because he was travelling by plane at the time.
The vehicles were assaulted as they headed north from Juba to the town of Bor.
“Three people were wounded. These are security guards of the first vice president,” State Minister of Information Jacob Akech Deng said.
“No soldier died and the convoy of the first vice president has reached Bor safely.”
Source: Al Jazeera and news agencies