The pair are due in court tomorrow in the northeastern town of Middelburg charged with assault and intent to cause grievous bodily harm, according to the court's clerk.
The footage was apparently shot on a mobile phone by one of the two white men involved in the incident.
The 20-second clip shows one white man shoving the black man, who makes distressed noises, into the wooden coffin and trying to force down the lid.
They are also accused of threatening to put a snake in the coffin.
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The video, which is undated, has spread rapidly across social media.
It was allegedly taken at a farm close to Middelburg town in Mpumalanga.
The Economic Freedom Fighters (EFF) opposition party said that it would rally outside Middelburg magistrates court on Wednesday to protest the alleged assault and racism in South Africa.
"The two white men... Beat up a black man, Victor Rethabile Mlotshwa, and put him in a coffin," the EFF said in a statement.
"This humiliation can be based on nothing else but his blackness, which means it is in actual fact a humiliation of black people as a whole."
Racial controversies have erupted regularly on social media in recent years in South Africa, which is still beset by deep-rooted inequality 22 years after the end of white-minority apartheid rule.