She had broken Olympic team mate Sarah Hammer's record in qualifying earlier and lowered it again in the final.
Kelly Catlin, who won gold alongside Dygert in the team pursuit, took the bronze medal.
Hosts the Netherlands also had to make do with silver in the women's madison won in superb style by British duo Katie Archibald and Emily Nelson.
Nelson was only drafted in after Eleanor Barker's crash in the omnium the previous day but proved up to the task as her and Archibald won eight successive sprints to finish 15 points ahead of the Dutch duo of Kirsten Wild and Amy Pieters.
Wild had been going for her third gold of the week.
For Nelson it was a first world title, having won silver with Barker in the madison last year in Hong Kong.
"It's going to take a while for that to sink in," she said. "It was really hard to see the scoreboard so I just kept going as though people were one point behind us."
Miriam Welte of Germany won the women's 500m TT, beating Russian Daria Shmeleva with Dutchwoman Elis Ligtlee third. Welte also won the women's team sprint.
Australia's Matthew Glaetzer beat Britain's Jack Carlin 2-0 in the men's sprint final.
(Reporting by Martyn Herman, editing by Pritha Sarkar)
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