A spokeswoman for the National Museum of Natural History said two females and a baby were tracked down at around 4:15 am (0315 GMT).
The zoo is 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.
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.
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