Samuels outpaced rivals Elizabeth May, of Luxembourg, and former world mountain running champion Kate McIlroy, of Wellington, to win the female elite race by almost 2min.
She crossed the finish line to a thunderous reception from her home crowd supporters, minutes before the heavens opened as the men's elite race got under way.
Heavy rain saturated the men for their race and made cycling treacherous in the slippery conditions.
New Zealand Under-23 champion and local favourite Tony Dodds, of Hawea Flat, tried to match Samuels' winning performance, but was outpaced on the final lap of the 5km run by Aucklander Ryan Sissons.
The thunderstorm arrived on cue for the men's elite sprint and provided a close-matched tussle for spectators who braved the elements, or managed to take shelter in the bars and cafes lining the race course.
Unlike the women's race, where Samuels took control early in the bike leg, established a strong lead and ran away on the final leg, the men's race provided action aplenty.
Dodds said the leaders were lucky to avoid a crash on the first corner of the bike leg as rain saturated the course.
Sissons said the conditions meant none of the competitors were able to break away during the 20km road cycle.
Four of the country's rising young triathletes battled it out to try and establish dominance.
Sissons and Dodds were joined by Clark Ellice, of Taranaki, and Martin Van Barnfeldt, of Wellington, as the group made the transition from cycling to running.
The four were evenly matched during the bike and first two run laps around Pembroke Park.
Sissons made his break on the penultimate lap.
"I surged away down the lakefront straight and made another push as we rounded the back of the park. I just pushed as hard as I could and managed to run away from there," he said.
Earlier, Samuels delighted local triathlon supporters with a dominating performance in the women's race, after she exited the water in third place.
"I was really happy to be strong on the bike. I caught up with the leaders out of the swim transition in the first half lap and picked it up from there."
Samuels finished strongly in the run to outclass the chasing May and McIlroy.
"Things went according to plan and I spent most of the race by myself," she said.
The Contact Tri Sprint Series moves on to Timaru in three weeks, where Samuels said she would compete.
Ahead of the Timaru tri leg, Samuels will spend the interim at 1500m above sea level at her mountain base home at the Snow Farm, on the Pisa Range, near Wanaka.
A high altitude training camp for New Zealand's elite triathletes is being held, with Dodds and many of the other competitors from last night's race also attending.
