Saeed Basanda, dressed in a blue T-shirt and with a white bandage wrapped around his left hand, has been identified as a 37-year-old Egyptian national.
His co-accused, Samuel Avamarkos, is identified in the charge sheet as a 47-year-old South African citizen.
They both registered the same addresses in the town of Cullinan, east of the capital, Pretoria, where the murders took place.
The case has been postponed to March 27 for the two to get legal representation and an Arabic translator, which they have requested.
The two were arrested after the monks were killed Tuesday at the Saint Mark the Apostle and Saint Samuel the Confessor Monastery in Cullinan, where a fourth person was also beaten with an iron rod before escaping to safety, according to police.
Members of the church, wearing black robes, were in the courthouse gallery and sat quietly as the brief proceedings took place.
According to the police, nothing was stolen during the attack and the motive remains unknown.
The Coptic Orthodox Church has its headquarters in Egypt and dioceses in several countries. It is one of the oldest Christian communities in the world and has been the target of deadly attacks by Islamic militants in Egypt and elsewhere.
However, attacks on places of worship are rare in South Africa.
The Coptic Orthodox Church named the monks killed as Monk Hegumen Takla el-Samuely, Monk Yostos ava Markos and Monk Mina ava Markos. All three were Egyptian nationals.
The Coptic Orthodox Church of South Africa said that el-Samuely was the deputy of the Coptic diocese of South Africa.
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