Michel Aupetit, the archbishop of Paris, welcomed 30 worshippers into the landmark gothic cathedral on Saturday.
A congregation mainly made up of priests and church employees stood in a side chapel behind the choir stalls, which officials had deemed a safe location.
It remains unclear when Notre Dame will officially reopen to the public.
The priests were permitted to gather for its annual Dedication Mass, to commemorate the cathedral’s consecration.
“This cathedral is a place of worship, it is its very own and unique purpose,” Mr Aupetit said.
One French priest called the service “a true happiness, full of hope.”
“We will rebuild this cathedral. It will take time of course — a lot of money, lot of time, lot of work — but we will succeed,” said Pierre Vivares, one of the congregation.
“Today it’s a small but a true victory against the disaster we have had.”
It is still unclear what caused the blaze, which began on the evening of 15 April.
The fire tore through the historic building’s roof, toppling the spire as shocked Parisians looked on.
Emmanuel Macron, the French president, has promised to rebuild Notre Dame in five years and a campaign to fund the effort has attracted promises of donations.
French billionaires, including Bernard Arnault and Francois Pinault, pledged to donate millions of euros to the cathedral in the aftermath of the fire.
But a spokesperson claimed bigger donors had yet to pay a cent towards its restoration.
“The big donors haven’t paid. Not a cent,” Andre Finot, a Notre Dame press official, said on Friday.
“They want to know what exactly their money is being spent on and if they agree to it before they hand it over, and not just to pay employees’ salaries.”
Some of the workers who are helping to repair the church were invited to Sunday’s service.
For security reasons Mr Aupetit and others wore hard hats and the number of attendees was restricted.
Other worshippers could watch the mass live on a Catholic TV station.
The recording of the service showed some burnt wood but a famous statue of the Virgin Mary appeared intact.
Franck Riester, France’s culture minister, said this week that Notre Dame remains in a “fragile” state, especially its vaulted ceiling, which is still at risk of collapsing.
Additional reporting by agencies