The service was broadcast live on a religious tv channel that showed images of the blue sky through the collapsed roof and the black rubble still clogging the building. Some of the workers rebuilding the church were also invited.
The mass was held a day before an annual celebration of the consecration of the church's altar, known as the feast of the Dedication of Our Lady, and Aupetit prayed to the statue of the Virgin Mary, saying that he was thankful to be there.
Two months after a fire engulfed the building in Paris, the service was celebrated by Paris Archbishop Michel Aupetit on Saturday in a chapel behind the choir, a place confirmed by construction experts as safe.
The Mass was held in a side chapel that was left undamaged by the fire, and the attendees were required to wear protective hard hats.
French Minister of Culture Franck Riester that only 9% of the $955 million in donations that had been promised to Notre Dame's reconstruction had actually been received, according to Agence France-Press.
People gather in front of Notre-Dame Cathedral in Paris.
TOPSHOT - Notre-Dame de Paris cathedral's rector Patrick Chauvet greets people arriving for the first mass of the Notre-Dame de Paris cathedral two months after the fire, on June 15, 2019 in Paris.
Pledges of some 850 million euros ($960 million) had been made from prominent French businessmen and ordinary citizens but only around 10 percent of that has been donated so far.
"It is with much emotion that we are here to celebrate the consecration of the cathedral", said Paris's archbishop Michel Aupetit, who led the service.
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The April 15 blaze caused the roof and spire of the architectural masterpiece to collapse, triggering a worldwide outpouring of sadness as well as the multi-million-euro pledges for reconstruction work.
It is still unclear when the cathedral will reopen to the public.
"There may be people who promised to donate then in the end did not", Riester said Friday.
Without giving further details, he added: "But more importantly, and this is normal, the donations will be paid as restoration work progresses".
French President Emmanuel Macron has set a goal to complete reconstruction within the next five years.
'The president was right to give a target, an ambition. "But obviously what matters in the end is the quality of the work".
The damaged cathedral. fix work is underway, but it expected to take years.
A temporary structure could be erected there to host worshippers while the cathedral is rebuilt.