He called on Christians in Nigeria, St. Theresa parishioners and those who lost loved ones in the bomb blasts to forgive those who ordered the killings and to not consider revenge.
The Islamist group Boko Haram took credit for a series of Christmas attacks, in which more than 40 people were killed.
Families, sympathizers, mourners and relatives of the deceased shed tears during the Mass when they saw the victims' coffins inside the church.
"Beyond forgiveness, let us pray for the conversion of those who have allowed themselves to be used by the devil to perpetrate such a diabolic act, targeting and killing innocent men, women and children," Archbishop Onaiyekan said.
He asked for constant prayers for those in charge of security of Nigeria, that they "will have the wisdom to know how best to tackle the problem on our hands and the courage to do what needs to be done.
Nigeria's bishops have described the Christmas bombings as the equivalent of a declaration of war against the nation.