According to the Sudan Tribune, his wife, who is also the Defense Minister, Angelina Teny, has also recovered from the disease.
The couple tested positive for Coronavirus three weeks ago.
The newspaper said a statement from Mr Machar's office said he was discharged on Saturday "having fully recovered".
The statement stated that they were discharged after the second COVID-19 tests conducted showed they were negative.
“The First Vice President, H.E. Dr. Riek Machar Teny-Dhurgon, and the Minister of Defense and Veterans Affairs, H.E. Madam Angelina Teny, have both been discharged today (Saturday) as having fully recovered from the Coronavirus (COVID-19),” the statement said.
“The two leaders are therefore expected to resume their daily active public office duties anytime soon, hopefully by Monday, 8 June 2020,” the newspaper quotes the statement as saying.