Footage shared online showing the brutal deaths of 20 Egyptian Copts and one Ghanaian Christian shocked the world in February 2015.
Commenting on the church's inauguration, Bishop Gregory Mansour from the Maronite Church in the US told the Catholic News Agency: "Any way that the Church of today can honour her martyrs is a blessing.
"The story of these 21 brave men is worth telling.
"In way too many places, Christians are under siege from the dark forces of extreme hatred, and their freedom is conditioned by this hatred."
The church has been built in the village of al-Our in Minya province, Upper Egypt, where the Egyptian Christians came from.
Relatives had hoped to bury the bodies of the victims during Thursday's ceremony; however, they are yet to be united with the remains of their loved ones.
Day labourers, the men were rounded up by armed militants during two separate abductions in Libya in December 2014 and January 2015.
During the abductions, ID cards were checked; workers registered as Muslims were set free while Christians were kept behind.
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