The haul from the robbery, mostly jewellery, was worth several million euros, police said.
The robbery took place at about 03:00 local time (01:00 GMT).
A spokesman for Kardashian said the star was "badly shaken but physically unharmed". No one else was hurt in the robbery, police said.
The spokesman told CNN the robbery was carried out by two masked men with guns, but other reports put the number of assailants at five.
Kardashian stayed at the residence, behind Paris's Madeleine church, at least once before, in 2014, before her marriage to rapper Kanye West.
Police were guarding the site on Monday.
"The loss amounts to several million euros, mostly jewellery. The total amount is still being evaluated," police said.
West was on stage at the Meadows Music and Arts Festival in New York at the time of the robbery. He abruptly ended his set, telling fans: "I'm sorry, family emergency. I have to stop the show."
It is unclear if the couple's two children, three-year-old daughter North and 10-month-old son Saint, were with Kardashian in the hotel room.
The star was in Paris for the city's fashion week.