In a video message, he described sexual violence as "one of the most shameful facts of our day".
The message was recorded during his recent visit to the Democratic Republic of Congo where he met victims and saw firsthand the work that churches are doing to help victims recover physically and spiritually.
He said the conflict-ridden DRC was at the "epicentre of a great deal of appalling violence in recent years".
The Archbishop voiced concern at the way in which sexual violence was being used as a weapon of war to "humiliate and subdue others" and had become endemic in many communities in the DRC.
Many churches in the DRC are supporting survivors of such abuse by providing them with medical care and trauma counselling, as well as working to combat the stigma victims face in their communities as a result of the violence they have suffered.
"The women in Congo, especially in this part of Congo, have suffered dreadfully because of this. And the connection between sexual violence of this kind and the spread of HIV/AIDS is one of the most shameful facts of our day," he said.
"Trauma is something which cannot be overcome overnight but when people feel they've been abandoned by families, by communities, because of the shame and stigma of HIV/AIDS, the church in this part of Congo has been there for them.
"For these people, who have been abused systematically, been raped, violated, abducted often at the youngest of ages – for these people, the church has been the family that mattered."
He urged churches and the international community to follow the example of the churches in DRC in their effort to end sexual violence.
"As we seek to confront the terrible scandal of sexual violence as one of the causes of HIV and AIDS, let's hope and pray that communities like the churches here will continue to fight as hard as they can against the stigmatising and marginalising that so reduce human dignity."
The Primates of the Anglican Communion have made tackling gender-based violence one of their priorities. At their meeting in Dublin in January, they committed themselves to taking action and wrote to their churches with guidance on how they could respond.