Warriner, a last-minute confirmation for the race, ran down a deficit of 1min 13sec coming off the bike to overtake Samuels on the second lap of the 5km run.
Defending champion Samuels had opened up the gap after a strong cycle leg, but Warriner's leg strength proved the difference over her younger rival as she ran home to finish with a lead of more than a minute.
Warriner's stamina to outpace Samuels was all the more impressive, given she raced six days ago in Tauranga and won the New Zealand Half Ironman Championship.
Lake Hawea athlete Tony Dodds shared some of Samuels' frustration, when he also found himself beaten into second place in the men's race - for the second year running.
Wellington's Martin van Barneveld ran away from Dodds over the final 100m to claim the win.
The men's race was a close affair, especially during an exciting cycle leg, where a leading bunch jockeyed for position during the 20km sprint through the township's streets and along the lakefront.
Dodds and van Barneveld came off their bikes together at the transition and quickly opened up a lead from a chasing pack during the first lap of their run.
They battled neck and neck during the second lap, before van Barneveld held off Dodds over the closing stages to clinch first place, while Austrian triathlete Andreas Giglmayer ran home to finish third.
Results:
Women: Sam Warriner, Whangarei, 1hr 2min 2sec, 1; Nicky Samuels, Wanaka, 1hr 3min 28sec, 2; Maddy Brunton, Te Awamutu, 1hr 6min 27sec, 3.
Men: Martin van Barneveld, Wellington, 54min 58sec, 1; Tony Dodds, Lake Hawea, 55min 1sec, 2; Andreas Giglmayer, Austria, 54min 27sec, 3.
