The womens race featured a small but competitive field led by Hill, who quickly proved her No. 5 ITU ranking in the opening stages of the swim.
After the swim, the field was split into two distinct groups. In the lead were Hill, Nancy Kemp-Arendt from Luxembourg, Haruna Hosoya from Japan, Kim Carter from South Africa and Sandra Soldan from Brazil.
Scotlands Stephanie Forrester, who was second in Rio, came out of the water at the head of the second pack, along with third-place finisher in Rio, Carlo Moreno from Brazil and Kiyomi Niwata from Japan.
Throughout the 40K bike portion, the first group continued to increase their lead on the chasing field and sped into the second transition almost two minutes ahead.
After a lightening-fast transition, hometown favorite, Hosoya, sprinted out in the lead with race favorite, Hill on her heels.
The two ran neck and neck for the first few kilometers of the 10K run, but Hills determination proved too strong for Hosoya as the Kiwi pulled ahead and never looked back.
The victory had special meaning for Hill, whose father died only a few days prior to the event she ran the race wearing a black armband and dedicated her finish to his memory.
On the mens side, it was a race of surprises with reigning junior world champion Atkinson proving the strongest contender on the day.
In the water, swim specialists Ricky Jorgensen from Denmark and Richard Stannard from Great Britain assumed their usual position at the head of the pack and led the field into the first transition.
The top two were joined in transition by Conrad Stoltz from South Africa, Johannes Enzenhoffer from Austria, Courtney Atkinson from Australia and Japan's Takumi Obara.
This lead group formed a strong pack on the bike and worked together to pull well ahead of all chasers, including top runners such as reigning world champion Dimitry Gaag from Kazakhstan and Simon Whitfield from Canada.
The first pack continued to increase their lead throughout the bike and sped out onto the run with almost two minutes on the much larger pursuing pack.
Atkinson, in only the second world cup of his career, assumed the lead in the first few kilometers and never looked back, leaving Enzenhoffer, Obara and Spaniard, Ivan Rana to fight it out for the other two podium spots.
At the end of the day, a surprisingly relaxed Atkinson cruised across the finish to capture gold with Enzenhoffer out-sprinting Obara to take second.
Atkinsons top spot ensures a continued bright future for Australian triathlon, and Obaras trip to the podium secured an amazing three podium places for host nation, Japan.
The World Cup series heads down under next weekend for round four on the Olympic course in Sydney, Australia.
Many nations, including Australia and the United States, are using next weeks race as a team qualifier for the Olympic Games, so competition will no doubt be fierce.
ITU WORLD CUP Ishigaki, Japan
1.5K swim, 40K bike, 10K run
1. Rina Hill (NZ) 2:01:40
2. Haruna Hosoya (JPN) 2:02:26
3. Akiko Hirao (JPN) 2:02:29
4. Steph Forrester (GB) 2:02:34
5. Machiko Nakanishi (JPN) 2:03:09
1. Courtney Atkinson (AUS) 1:48:06
2. Johannes Enzenhofer (AUT) 1:48:15
3. Takumi Obara (JPN) 1:48:18
4. Ivan Rana (ESP) 1:48:26
5. Roland Knoll (GER) 1:48:27
9. Dimitry Gaag (KAZ) 1:49:19