In his homily, Archbishop Aupetit stressed the purpose of Notre Dame as a place of Christian worship, and not an ornament of the secular state.
The appointment by Bishop Barres was effective June 1.
Pope Francis also visited the Roma, or Gypsy, community, asking forgiveness for times when the Church excluded them.
Read the text of Bishop Barres commencement remarks here.
The field of flags honors service members, living and deceased. It will remain in front of the school until flag day.