The men reportedly face charges of "kidnapping and assault with intent to cause grievous bodily harm".
The 20 second video showed a white man forcing a black man inside a coffin, and threatening to pour petrol over him and set it alight.
The video, which was circulated on social media, has caused widespread outrage.
The men are due to appear in the Middleburg Magistrate Court on Wednesday.
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The victim, Victor Rethabile Mlotshwa, was resisting and could be heard screaming as his captors - named as  Willem Oosthuizen and Theo Martins Jacksonthen - threatened to put a snake inside the coffin.
It is not clear what happened to Mr Mlotshwa after the filming ended.
The opposition Economic Freedom Fighters (EFF) said: "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."
The incident is said to have taken place at JM De Beer Boerdery next to Komati Power Station, close to Middelburg in Mpumalanga, the eNCA website reported.
South Africa has seen a spate of racially charged incidents in recent history, such as videos of white people calling black people monkeys, but the coffin case has sent shockwaves across the country - due to its horrific nature.
It is not clear when the video was shot but the incident has opened old wounds, with some likening it to the torture black people endured at the height of white minority rule here.
But is South Africa more racially divided now?
The South African Human Rights Commission does not believe so but adds that more cases are being reported - mainly because social media has helped break the silence and made it easier for people to share their stories.
The commission has also found that people are more educated about their rights and what recourse they can take.
As a result of the well-reported incidents in the media, South Africa is in the process of introducing specific laws to prosecute race related crimes.
Two white South Africans have been arrested over a video in which a black man was forced into a coffin.