The Independent Police Investigative Directorate (IPID) said the bail hearings marked the first court appearance of law enforcement officers accused of brutalities during the coronavirus lockdown in the country.
The IPID said it arrested 13 police officers and three private security workers last week in relation to the incident.
They have all been released on bail pending a formal indictment in August.
The bail hearings marked the first court appearance of law enforcement officers accused of brutalities during the coronavirus lockdown in the country, the IPID said.
The man, who has not been named, was held along with three others in April 2020 in a Johannesburg suburb for breaching lockdown rules, the Independent Police Investigative Directorate (IPID) said in a statement.
He was then allegedly assaulted by the police officers and members of a private security firm, before being taken to a police station, where he complained about stomach pains, it said.
"An ambulance was called in, the paramedics declared the one civilian dead," the police watchdog said in a statement, adding that a murder investigation was subsequently opened.
South Africa imposed one of the strictest confinements in the world during the pandemic but was the continent's hardest-hit country, reporting more than four million infections and 101,935 fatalities.
Police violence during the pandemic confinement, triggered national outrage and some protests in 2020, with rights groups reporting an increase in the use of lethal force.
Some 115 people were reported to have died in custody, according to Amnesty International, which welcomed the arrests but questioned why they took so long.
All of those victims "deserve justice," Amnesty International South Africa's executive director Shenilla Mohamed said in a statement, calling for swifter investigations.
"We will not see an end to these incidents unless those responsible are held accountable," she said.