A spokeswoman for the National Museum of Natural History said two females and a baby were tracked down at around 4:15 am.
The zoo was expected to reopen around noon.
“The professionalism of the wildlife teams at the Paris zoo allowed for a happy ending … we are analysing the precise circumstances of the incident,” the spokeswoman said.
The baboons remain in the area of the “grand rocher”, a landmark central mountain inaccessible to the public at the zoo in the lush Vincennes area of the French capital.
The breakout was first noticed by a zoo worker, who saw the primates gathering in a service corridor used by personnel late Friday morning.
Safety procedures were immediately triggered, the zoo said in a statement, with a total of 60 firefighters, 20 police and all of the zoo's staff mobilised to capture the animals.
None of the baboons reached public areas and the evacuation was ordered as a precaution, the zoo said.