Just 30 people were permitted entrance, and all the attendees including Paris Archbishop Michel Aupetit had to wear hard hats throughout the service.
Exactly two months after fire ravaged the landmark Gothic building in Paris, the service was celebrated in a chapel behind the choir, a place designated by construction experts as safe.
French Culture Minister Franck Riester said this week that the cathedral remains in a “fragile” state, especially its vaulted ceiling, which is still at risk of collapsing.
Numbers allowed to attend were kept small for security reasons, with the 30 people present made up mostly of priests, canons and church employees along with some of the workers rebuilding the church.
Other worshippers could watch the Mass live on a Catholic TV station.
Footage showed some burnt wood still in the church but a famous statue of the Virgin and Child appeared intact behind wooden construction planks.
The annual Dedication Mass commemorated the cathedral’s consecration as a place of worship.
“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”.
Father Pierre Vivares said: “We will rebuild this cathedral. It will take time of course – a lot of money, a lot of time, a lot of work, but we will succeed. Today is a small but true victory against the disaster we have had.”
It is still unclear when the cathedral will reopen to the public.
French President Emmanuel Macron has set a goal of rebuilding it in just five years, which many experts consider unrealistic.
The French parliament is debating amendments to a new law that would create a public body to expedite the restoration of the cathedral and circumvent some of France’s complex labour laws.
Press Association contributed to this report