In an exclusive interview with Premier, His Grace Most Revd Thabo Makgoba said he hopes the country can finally move on after the change.
He's speaking after an appeal court judge overruled a previous decision that Oscar Pistorius had committed culpable homicide when he killed his late girlfriend Reeva Steenkamp, and changed it to murder.
This means Oscar Pistorius must leave house arrest and go back to prison.
South African law states a minimum of 15 years for murder, however judges can use discretion with this.
Oscar Pistorius spent one year of his five-year sentence in prison for his previous conviction of culpable homicide before being moved into house arrest, where he was until today's verdict.
The former Paralympic athlete shot through a closed bathroom door four times, killing his late girlfriend inside. He has always said he believed it was an intruder and not her.
He can appeal on the grounds the new ruling breaks his constitutional rights, however legal experts have said it is unlikely this would be successful and that is he is probably going back to prison.
His Grace Thabo Makgoba also said he is praying that Oscar Pistorius will continue to receive spiritual support from Christians when he receives his new sentence, as well as the family of the late Reeva Steenkamp.
The leader of Anglicans in South Africa also said the murder conviction sends a signal to women in South Africa highlighting the unacceptable nature of domestic abuse.
He told Premier's News Hour: "I want to send my condolences to Reeva's family, and equally I want to pray for all involved in the Pistorius family during this very trying time.
"My prayer is, particularly in the week just before we remember two years of Nelson Mandela's passing on, we will have magnanimity of South Africans, we will pray that justice will be done but we will start the process of healing through whatever the courts will lead us.
"Whether he's in or out [of prison] the pastors will still offer him [Pistorius] the necessary pastoral support without necessarily condoning what has happened, that the pastors will continue to offer Reeva's family the pastoral and spiritual support.
"During this month of... activism against domestic abuse, we really need to be characterised by the rule of love and really need to honour each other. We really need to step away that demean both women and children and that the rule of law should take its course.
"Domestic violence is just too high. One woman abused is one too many."
Listen to Premier's Hannah Tooley speaking to His Grace Most Revd Thabo Makgoba.
