The front-rower, who has one Test cap for South Africa, impressed during a three-month stint at Thomond Park at the end of last year and was invited back.
Munster manager Shaun Payne welcomed the deal and said: “Wian proved an extremely effective player with a massive work ethic and the ability to quickly adapt to the challenges placed before him, he was also very popular with the other squad members.
“We are delighted he has agreed to return and know he will be a hugely positive influence, both on the field and as a role model to the young Munster front rows who are coming through.”
The 27-year-old had reportedly become disillusioned by the repeated shunning he has received from Springboks selectors.
“Wian played for Munster in the Heineken Cup during his off-season after South Africa’s end-of-season tour last year,” the player’s agent, Stephan Weyers, told South African newspaper Volksblad.
“They were really impressed by his scrummaging and commitment, and have made a good offer. We told (Cheetahs coach) Naka (Drotske) early on that we are considering another offer and were open with him from the outset.
“Wian would love to come and end his career at the Cheetahs.”
While Du Preez’s departure will be a blow for the Bloemfontein franchise, Weyers confirmed that another Springbok, CJ van der Linde, would be returning to the city where he started his career in the early 2000s.
The 29-year-old, who was part of the 2007 World Cup-winning team, is determined to again make the national team for the defence of the title in New Zealand next year.
Van der Linde, a veteran of 58 Tests, will join from Magners League finalists, Leinster, where he has been since 2008.
Over the past weekend, he was also included in the South African side that will play Wales in Cardiff on June 5. Weyers added: “CJ is delighted to have the opportunity of pulling on the Cheetahs jersey again and is looking forward to playing in the Currie Cup again with old team-mates and close friend Juan Smith.
“We are indebted to SA Rugby as they made CJ’s move to South Africa financially viable by offering him a contract until after the World Cup.”