The 21-year-old quantity surveying student's performance also helped the Port Elizabeth-based campus to the overall men's crown in the three-day Surfing South Africa sanctioned event, which culminated on June 27.
The University of Cape Town's Daniel Wilson and Varsity College's Wade Simkiss made up the rest of the podium.
Du Plessis, who grew up in East London and surfed his way to third place at the national championships as an under-16, said he was stoked with the victory.
"We enjoyed some big waves, between four and six feet, and, although the competition was quite tight, it all came together for me in the final."
Defending women's champion Roxy Giles, from NMMU's George campus, bested Varsity College's Nicole Pallet in the final while UCT's Jessica Lee took third.
The Madibaz's success was made even sweeter when Du Plessis, teammate Dane van Greunen and Giles were selected for the Ussa national team that will participate in various international university surfing competitions.
NMMU George sport manager Hugo Loubser said he was very proud of the team, especially the men who had reached all of their objectives.
"Our PE campus did really well, especially after losing Josh Saunders (the team's number one) very early on. The George men's team have less experience and exceeded our expectations by beating Stellenbosch for fifth."
Overall victory across the men's and women's categories went to defending champions UCT with NMMU PE second and Varsity College third.