Eilidh MacLeod, 14, remains unaccounted for but her friend Laura MacIntyre, 15, is said to be in a "serious condition" in a Manchester hospital.
Bishop Brian McGee joined local priest Fr John Paul MacKinnon in visiting relatives and then saying Mass for the families.
They later visited Castlebay High School, where both girls were pupils, to speak to teachers and staff.
Bishop McGee said: "This is a time of terrible anguish for the MacLeod and MacIntyre families.
"Spending time with the relatives of both girls was a reminder of the human cost of acts of terror.
"Such acts leave families broken, lives scarred and innocence destroyed, my thoughts and prayers are with the families at this traumatic time."
Twenty-two people were killed in the attack at Manchester Arena. A further 64 are being treated in hospital.