Viljoen crossed the finish line along the Esplanade in a time of 2:34:35, with his teammate Francois Geldenhuys finishing third on the day in 2:35:53, 43 seconds behind second-placed Donovan O'Reilly.
Another Madibaz rider, Waldo Gronum, led a bunch sprint to the line to take fourth place overall in 2:41:19.
Also in that mass sprint was clubmate Allison Hertel, who was just pipped to the post in the women's race by defending champion Anriette Schoeman.
Former Buffalo City resident Viljoen led a team of six NMMU riders for the 100km road race, in which he placed second last year.
Now based in Port Elizabeth, he said that although it was an away race for the team, it felt like a home race to him.
"Knowing the route well and how the wind usually blows made it strategically easier for me and I used it to my advantage," said Viljoen.
The 30-year-old said he believed the organisers had created a course that was safe, challenging and tested riders' abilities in all sectors.
"The route is very hilly in the first half, which gives an opportunity to the climbers. However, after the turn it is always fast and the sprinters can reel in most breakaways."
Viljoen's major challengers, O'Reilly and Royce Griffin, attacked early on and were joined by Geldenhuys and teammate Christiaan van Aardt.
"I saw the gap was being closed halfway up the Hemingways Casino climb (the first major ascent) and managed to get across and win the king of the mountains on top.
"The group came back together again before Francois attacked again and went up the road for about 5km before the bunch closed him down," said Viljoen.
The second big climb began 20km into the race with Griffin putting in a sizeable effort while Viljoen and Van Aardt stuck to his back wheel.
"Royce got dropped halfway up the climb and the two of us opened a gap of about 40 seconds before Donovan and the bunch closed the gap to us," said Viljoen.
The former Port Rex Technical High School learner said the decisive break was orchestrated when he, Geldenhuys and O'Reilly joined forces.
"We worked well together to build a gap of two minutes and 40 seconds on the chasing bunch.
"We started attacking Donovan about 75km into the race on the rolling hills but unfortunately Francois got dropped.
"On the last climb, about 6km from the finish, I attacked and managed to hold Donovan off to the finish," he said.
Viljoen said the Madibaz cycling squad were aiming to reach new heights this year and really excel as a team.
"This year we have a good mix of experience and youth and our focus will remain on local races and the surrounding provinces," he said.
NMMU's Anja Gerber and Bradley Gouveris claimed victory in the junior categories, while Mandy Akom triumphed in the over-50 category.
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