Saint-Etienne-Du-Rouvray Mayor Hubert Wulfrance said Hamel's memory "prevails over this so special moment, split between endless emotion and hope in the future.
"We bear the tragedy of this July 26, 2016, as an indelible scar on our common history, our national history," he said to a crowd that included local Muslims invited to take part in the community event.
The Mass, attended by parishioners and other residents, was preceded by a penitential rite to restore the sacred nature of the church. A local imam and the head of the regional Muslim council were among the attendees.
Muslims from France and Italy attended a Mass the weekend after the July attack in a show of tolerance and solidarity.
Archbishop Dominique Lebrun presided over Hamel's funeral Massat the Rouen cathedral, a service attended by President Francois Hollande and Prime Minister Manuel Valls. In a show of inter-faith solidarity, Muslims and Jewish mourners were among the attendees.
France has been the target of several attacks by IS militants in the past year.
Just 12 days before Hamel's murder, another IS jihadi drove a cargo truck through a Bastille Day crowd in the Mediterranean coastal city of Nice, killing 86 people and injuring hundreds more.
And next month, France will mark the one-year anniversary of the worst terror attack in its modern history, when a series of coordinated attacks across Paris and its northern suburb left 130 people dead and hundreds injured.
In September,Pope Francis honored Hamel during a Mass at the Vatican, calling him a martyr and urging people of all faiths to denounce killing in the name of religion as "satanic."
On Sunday, Archbishop Lebrun told the church gathering that the pope has waived the five-year delay before a sainthood process can begin.