The 400m freestyle final followed a similar course to the 800m on the opening night, with Costa, the world short course champion over the distance, jumping out from the pack to go through the 200m in 1:57, on world record pace.
Boyle eased clear of Belmonte, still 1.5 seconds behind Costa, but gradually whittled away at the lead. She edged in front at the 350m mark and stormed away, showing outstanding pacing with 16/100th of a second separating each 50m split after 28 seconds for the opening two lengths.
Earlier Boyle clocked 4:04.30 to qualify third fastest in the heats behind World Cup overall leader Katinka Hosszu of Hungary and Bemonte.
Fellow Kiwi Cameron Simpson, the Gold Coast-based Cantabrian, was 10th fastest in 22.13s in heats of the 50m freestyle, just missing out on a place in the final.
The FINA World Cup moves to Tokyo on Saturday and Sunday local time, before the final two days of the circuit in Beijing on November 13 and 14.
Day 2 Results, finals:Women 400m freestyle: Lauren Boyle (NZL) 4:00.78, 1; Melanie Costa (ESP) 4:02.24, 2; Mireia Belmonte (ESP) 4:02.70, 3.