The Madibaz, who won the title from 2010 to 2015, shared the runners-up spot with Vaal University of Technology behind champions Walter Sisulu University.
On an individual level, NMMU's Teboho Zongola and Adre Weideman were chosen for USSA teams that will take part in international tournaments.
The 21-year-old Zongola, a marketing student who competes in full contact, will head to Russia in December while Weideman, a human movement science student, will compete in the semi-contact discipline at the World Student Games in Taipei next August.
Zongola, who hails from Matatiele in the Eastern Cape, was delighted with his selection, but added that he had plenty of room for improvement.
"The tournament was quite hectic, but I'm happy with my performance and the team's overall showing. My best effort came on the second day in the knockdown category when I had four fights and lost only the last to come second."
He said he was overwhelmed after learning of his selection.
"But this is something that I have been aiming for and Russia will be another learning experience."
Weideman, a 19-year-old from Korsten in PE, was encouraged by her parents to take up the sport and has been competing since 2006.
She has been selected for national teams since 2009 and is looking forward to attend the World Student Games after missing out in 2016.
"I was chosen last year to go to Portugal, but, unfortunately, it clashed with a number of other commitments," said Weideman, who won bronze in the kumite category.
"But now I have another chance and I'm hoping nothing happens this time so I can make up for last year's disappointment."
She said the tournament had been much tougher than in previous years, "which was good because it kept me on my toes".
Madibaz Sport's karate chairwoman Hlubikazi Zibi said the squad showed dedication and put in a lot of hard work.
"We congratulate them for giving it their all and we would like to recognise sensei Gcobani Maxama for his leadership and continued support."
Madibaz Sport karate manager Bernard Petersen said they were extremely proud of what the squad had achieved over a long period of time.
"Since 2005 we have never ended lower than second in the USSA tournament and it's a tribute to the hard work the students and coaches have put in over the years," he said.
"For example, Sensei Maxama has been very committed to getting the best out of our karatekas. He was a student himself so he understands what needs to be done to perform at a top level."
CAPTION: NMMU-Madibaz karatekas Teboho Zongola and Adre Weideman have been selected for national student teams after the recent University Sport South Africa tournament in Pretoria. Photo: Supplied