Sheikh Mohammad bin Zayed Al-Nahyan, Abu Dhabi's crown prince and deputy supreme commander of the UAE armed forces, ordered that the mosque be renamed to "consolidate bonds of humanity between followers of different religions".
Reverend Canon Andrew Thompson of St. Andrew's Church, near the newly renamed mosque, expressed his happiness in an interview with Gulf News.
He said: "We are delighted that we are celebrating something that we have in common between both our faiths."
Mary - who is called Maryam in the Quran - is the only woman with a chapter named after her in the Muslim holy book. While Muslims believe that God chose her above all women in the world to give birth to Jesus, they do not regard Jesus as the son of God.
The UAE's official religion is Islam but the nation's constitution guarantees the freedom to practice all religions.
Jeramie Rinne, senior pastor of the Evangelical Community Church in Abu Dhabi, said in an interview with The Cable that the mosque's renaming indicates the importance of the UAE's stance on religious tolerance.
He explained: "The UAE continues to set the pace in this region for peaceful coexistence and cooperation.
"We are very encouraged and feel blessed to be a part of this nation."
