He returned earlier to the capital, Juba, to take the post in a new unity government led by President Salva Kiir.
Tens of thousands have been killed and about two million people left homeless in the conflict in South Sudan, which became independent in 2011.
Mr Machar fled Juba at the start of the civil war in December 2013. Malakal: The city that vanished in South Sudan. READ MORE OF THIS STORY