After receiving criticism ahead of Sunday's event, church leaders said inter faith champion Monawar Hussain will speak after the service at St Mary's has finished.
The original advert suggested he would deliver the sermon during the service.
The invitation had received criticism from some online.
Writing on the Anglican blog Archbishop Cramner, Adrian Hilton said: "He will no doubt be preaching about love, peace, reconciliation and tolerance, all of which would be laudable topics for an inter-faith lecture or post-worship meditation.
"But by inviting an imam to preach not just a sermon, but a Eucharistic sermon, it is hard to understand how this glorifies the crucified Son of God; how it honours those martyrs who died renouncing theological error and deception; and how it respects a sacred act of divine worship which is supposed to be conducted according to the rites and formularies of the Church of England."
In response a spokesperson for the Diocese of Oxford said: "Monawar Hussain MBE DL will deliver the University Sermon following the Eucharist at St Mary's this Sunday. He is most welcome.
"Founder of the Oxford Foundation and the Muslim Tutor at Eton College, Monawar is well known to many in Oxford and he joins a long list of those invited to preach the University Sermon by the Vice Chancellor.
"Monawar is not the first person from another faith community to be invited to preach the University Sermon, his presence on Sunday reflects the strong commitment of the Church, University and other faith communities to interfaith engagement."
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