Santos was one hundredth ahead of American Andrew Michael who finished third.
Nicholas Santos has won several World Cup golds in the short course.
However, he has never been at the top of the podium in a long distance World Cup.
There have been four medals, three silver and one bronze, all in the 50 meter butterfly.
Water made the American Caeleb Dressel.
It was the 25-year-old's 15 World Cup gold medals in his career and his second in as many days.