Pheiffer, 33, edged out Mecer-NMMU's defending champion Conrad Viljoen in a thrilling dash to the line after a solo breakaway by the latter was thwarted in the closing stages.
Ronnie Scheffer (Mecer-NMMU) snatched the final podium position ahead of Brent Pheiffer (Walmer) and Johannesburg's Sam de Swardt (Toyota-Cycle Lab).
The leading bunch, consisting of 12 riders after five were tailed off in the run-in to the finish, crossed the line in a fast two hours 27 minutes and 24 seconds.
Toyota-Cycle Lab's Lindi Erasmus won an equally close women's race in 2:39:09. Walmer's Allison Hertel was second in the same time with Friendly City Cycles' Ingrid Brown third in 2:47:59.
Cramping towards the end
"I was working for Brent, but he started cramping towards the end and told me I should go for the sprint if I had the legs. That is when I realised it could be my day," said an ecstatic Pheiffer, who recorded his first win since returning to top-level racing three years ago.
"My aim was to turn into the home straight in the first three positions, so I started moving towards the front over the final two kilometres. I turned first, with Conrad on my wheel, and was able to hold him off.
"I knew that I was sprinting well, but I haven't been climbing well enough to make it count. I've been riding a lot of hills recently and it seems to be paying off."
Viljoen was responsible for the day's major move after attacking on the Maitlands climb at the 45-kilometre mark and staying clear for more than 40 kilometres.
He built a maximum lead of one minute, but was always going to struggle to keep off an attentive chasing bunch and was finally hauled back with less than 10 kilometres to go.
"I felt that if we worked together and kept a fast pace on the climbs to minimise his advantage, we would have a good chance of closing the gap once we hit the flat sections on Seaview Road," said Pheiffer.
He got his wish, but was one of several to succumb to the fast pace set set by Toyota-Cycle Lab's Earl O'Reilly and Masters and Ladies' Pascal Pau. "I didn't panic and was able to reintegrate with a few others on the downhill towards Seaview."
Pheiffer was full of praise for Viljoen's effort, saying he would've been a deserving winner. "I don't know how he managed to stay ahead for so long. He rode like a machine."
