"It's our first time [winning a world championship] in an Olympic-class boat, which is good looking to our main goal of the Olympics.
"We always knew there were some fast-starting crews, so we tried not to concentrate on what others did and just wanted to row our own race, which paid off in the second 1000m."
Gowler, 23, and Prendergast, 25, have more than an Olympic cycle of experience together in New Zealand's elite programme.
The duo won what was then the non-Olympic coxless four in 2014 with Kelsey Bevan and Kayla Pratt.
They earned silver in the pair and eight at the 2015 world championships but at the Rio Games they were replaced in the pair by Rebecca Scown and Genevieve Behrent, and asked to focus on the eight.
Elsewhere, Jackie Kiddle and Zoe McBride took silver in the lightweight double sculls and Jamie Hunter and Tom Murray earned bronze in the pair.
Kiddle and McBride won both their World Cup finals at Poznan and Lucerne, but the world championships added another layer of pressure.
Romania survived in the second 1000m to pip the New Zealanders by 0.21s, as the Kiwis dueled with the United States in their adjacent lane.
"It's one of the better races we've put out," Kiddle said. "To hear it was that close was pleasing for us. We pushed ourselves to the line.
"For the first 500m we tried to row our own race and I think we did that [to sit fourth]. We pushed at the 500m mark to claw back what we lost."
Hunter and Murray were involved in what was arguably the race of the day.
Italy produced a withering final 200m to overtake and defeat Croatia by 0.34s. New Zealand, the victors at the Lucerne World Cup, were a further 4.29s back.
"We gave it our best shot, but the Italians and Croatians were something else in the second half," Murray said.
"We probably didn't have that extra gear going through the kilometre mark. We improved on our start from the semi, but they just pulled away."
Yesterday Matt Dunham picked up silver in the non-Olympic lightweight single sculls.
New Zealand have five further medal contenders on tomorrow's final day of racing with both eights, double sculls and single sculler Robbie Manson in action.