The South African-born back row, who has operated at flanker and Number Eight, has made a total of 59 appearances for Blues and scored three tries.
Pretorius, who has won two caps for Wales after his debut during the summer tour last year to Japan, also captained Blues during the 2012/13 season.
Phil Davies, Director of Rugby at Blues, said: "Andries has been a fantastic professional during his time with the Blues. He is a real team player, a very popular member of the squad and has been a wonderful servant to our region.
"I have known of Andries since his time at Hartpury College and valued his knowledge and determination to make a real impact in the game.
"Andries has always been willing to pass on his experience to the younger players in our squad and during a time of change at Blues over the last few years he has done a great deal to help develop the right environment and mentality here.
"We will naturally be sad to see him leave at the end of the season and he will go with our best wishes, but we have a number of young players in the back row who are now eager to step up. The likes of Macauley Cook, Rory Watts-Jones, Ellis Jenkins, Thomas Young and Luke Hamilton are talents who have performed well this season.
"We are also actively recruiting in the market for new back row options as we want to add yet more experience to the young players who are making such a big impression for us."
Pretorius said: "I have really loved my time at Cardiff Blues and it has been an absolute honour to play for and captain such a great team.
"I have made many friends here over the last few years and the fans have been fantastic in their unwavering support.
"I will continue to give Cardiff 100 percent, like I have always done, until the end of the season and we have many big games and challenges to look forward to in both the Heineken Cup and RaboDirect PRO12."