"Being united is a response to the act of horror and barbarism," he said.
The Notre Dame church in southwestern Bordeaux also welcomed a Muslim delegation, led by the city's top imam Tareq Oubrou.
It's an occasion to show [Muslims] that we do not confuse Islam with Islamism, Muslim with jihadist," said Reverend Jean Rouet.
The Muslims were responding to a call by the French Muslim council CFCM to show their "solidarity and compassion" over the priest's murder on Tuesday.
About 2000 people, including Muslims, attended Mass at Rouen Cathedral (AFP/Getty Images)
"I'm a practising Muslim and I came to share my sorrow and tell you that we are brothers and sisters," said a woman wearing a beige headscarf who sat in a back pew at a church in central Paris:
Giving her name only as Sadia, she added softly: "What happened is beyond comprehension."
Prime Minister Manuel Valls called on Sunday for a new "pact" with the Muslim community in France, Europe's largest with around five million members.
"Islam has found its place in France ... contrary to the repeated attacks of populists on the right and far-right," he said, condemning "this intolerable rejection of Islam and Muslims".
Also on Sunday, dozens of prominent Muslims published a joint letter warning that "the risk of fracturing among the French is growing every day."
The signatories, who included academics as well as medical professionals, artists and business leaders, pledged: "We, French and Muslim, are ready to assume our responsibilities."
Muslims attend Mass at a church at Santa Maria of Caravaggio in Milan ((Pier Marco Tacca/Getty Images)
Both of the 19-year-old attackers - Adel Kermiche and Abdel Malik Petitjean - had been on intelligence services' radar and had tried to go to Syria.
Syrian refugee suspect released
Meanwhile, a Syrian refugee who was taken in for questioning after a photocopy of his passport was found at Kermiche's house has been released, a source close to the investigation said.
"Nothing suggests he had any involvement" in the attack, the source said.
However, Petitjean's 30-year-old cousin was to appear before an anti-terrorist judge later on Sunday.
Prosecutors said they have asked that the suspect, named as Farid K, be charged with "criminal association in connection with terrorism".
The suspect "was fully aware of his cousin's imminent violent action, even if he did not know the precise place or day", the Paris prosecutor said in a statement.
Media reports, meanwhile, said investigators had established that Petitjean and Kermiche met through the encrypted messaging app Telegram.
Kermiche described the modus operandi of the attack on the priest in an audio posted on Telegram just a few days beforehand.