The 15-year old primate made headlines on Tuesday after escaping from a hospital where the procedure had been due to take place.
The baboon had two female companions with him for emotional support who also escaped.
After around two hours of freedom running around the inner city, the trio was eventually recaptured by police and animal welfare experts.
Authorities say a lock failed on the truck or crate transporting the baboons and they were able to open it.
State health minister Brad Hazzard confirmed the vasectomy had been performed, (Vasectomy is a surgical procedure for male sterilisation or permanent contraception).
“Baboon ‘Houdini’ update: vasectomy has been completed this morning as planned.
“ Procedure went well. He is now sleeping/resting.
“His two female family members are relaxed and happy,’’ Hazzard said in a tweet.
Mr Hazzard earlier in the week rejected claims the animals were being used for research into human-baboon hybrid organs.
On Tuesday he told reporters the baboon was having a vasectomy because there’s no desire for him to continue to breed for the troop, and the other option was to move him from the troop.
“This way, he can stay with his family through until old age,’’ Hazzard said.
The baboons are involved in research on reproductive health, kidney disease and gestational diabetes and will be returned to their western Sydney colony after the male recovers, Australian Associated Press reports.