Pretorius, 32, had struggled to recover from a back injury all season and, acting on medical advice, decided to call it a day.
The former Springbok and Blitzbokke captain won a Currie Cup title and back-to-back Super Rugby titles after joining the Pretoria side from the Lions in 2008.
Pretorius admitted it had been a difficult decision to call an end to his career.
"I was so blessed in the 14 years of top flight rugby I played," he said.
"Words cannot describe the pride with which I pulled on my playing kit every time I could go out there, whether it was in red, blue or green," he said.
"I injured my back again during rehabilitation, and after seeking the opinions of specialists, I was advised to quit, so my retirement comes earlier than planned.
"I could not have played my last game at a better place than at the Bulls.
"To win trophies and play with legends of the game was a special privilege."
Heyneke Meyer, the Blue Bulls' head of rugby affairs, said Pretorius' retirement came as sad news for the union.
"Jaco was not only a quality player with a proven record when he joined us - he also provided leadership and a great ability to put the team first," Meyer said.
"His arrival in Pretoria and the success the Bulls and Blue Bulls had after that, with him as a regular starter, was no co-incidence.
"He will be missed and remembered by those who were lucky enough to play with him."
Pretorius played in 48 Super Rugby matches and 87 provincial games for the Lions and the Bulls, as well as two Tests, 23 international Sevens tournaments and two games for the Barbarians.