"As brutal and unfair and horrible as Jacques' death was, we have to look deep into our hearts to find the light," said Rouen Archbishop Dominique Lebrun.
Some 2,000 mourners packed the soaring Gothic sanctuary, with hundreds more watching the ceremony, which began minutes after a heavy rainstorm, on a giant screen outside.
A section of pews in the 11th-century cathedral was filled by residents of Saint-Etienne-du-Rouvray, the nearby industrial town where the two jihadists, both 19, slit Hamel's throat as he celebrated mass in an attack that shocked the country as well as the Catholic Church.
Another red stole was set atop a white priest's vestment lying over Hamel's coffin.
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In a show of inter-faith solidarity, Muslims and Jews were among the mourners.
"It was a duty," Hassan Houays, a Muslim maths teacher from Saint-Etienne, told AFP. "We are here so that we can get along together."
Reconciliation was an overarching theme of the mass, which recalled Jesus urging his followers to "love your enemies and pray for those who persecute you."
Archbishop Lebrun said the Christian, Muslim and Jewish communities have "decided to come together to say 'never again'."
Along with churches across France, the Rouen cathedral had on Sunday opened its doors to Muslims wishing to show their solidarity after the grisly attack, with the visitors paying a moving tribute to Hamel while denouncing radical Islam.
French Interior Minister Bernard Cazeneuve, whose portfolio also includes inter-faith relations, led the political delegation to the mass.
As on Sunday, security was tight for Hamel's funeral, with around 20 riot police vans stationed around the cathedral and police closely checking mourners' bags and backpacks.