Warriner built on her lead out of the water and by the time she hit the 5.5km mark of the run she had a nine minute buffer.
At that stage she looked like she had the race all sewn up, the only problem was nobody remembered to tell Niwata, another former ITU athlete, who had the lead down to just two minutes at the 17.5km mark.
In the end she ran out of tarmac and finished 1:06 behind Warriner.
Meanwhile, former ITU athlete Courtney Atkinson set up his first Ironman 70.3 win with a strong bike leg in brutally windy conditions.
Atkinson withstood a strong finish from fellow London Olympian Brad Kahlefeldt to claim the men's title with another Australian, Tim Reed third ahead of Ironman World Champion Pete Jacobs.
New Zealand long distance champion Graham O'Grady (Taupo) led on the bike in a four strong group but succumbed on the run as the pace went on.
In the end it was the former ITU boys who had speed to burn with Atkinson taking the top spot on the podium, with Kahlefeldt only a minute behind after being four minutes back off the bike.
Meanwhile, Bevan Docherty (Taupo) made it a winning double for Kiwis, with his victory at Ironman 70.3 in Boise, USA.
Docherty is showing the benefits of his long and successful ITU career as he transitions into longer distance racing, aiming at Kona later this year and a tilt at the Ironman world championships.
The two-time Olympic medallist who is in his first season out from the Tri NZ HP Programme was all class in posting the quickest bike and run splits on the day, winning by close to two minutes from Brent McMahon (CAN) and Josh Amberger (AUS).
Results, ironman 70.3 Cairns, women: Samantha Warriner (NZL) 4:39:18, 1; Kiyomi Niwata (JPN) at 1:06, 2; Ange Castle (AUS) at 6:22, 3.
Men: Courtney Atkinson (AUS) 3:56.33, 1; Brad Kahlfeldt (AUS) at 51sec, 2; Tim Reed (Aus) at 3:09, 3.