Trott, who was part of the quartet that finished first in the women's team pursuit event, finished the individual six-event competition on 15 points.
That put her level with Kirsten Wild of the Netherlands, but 21-year-old Trott won the title on countback.
Triple Olympic champion Jason Kenny claimed a silver in the men’s keirin event to go with his sprint bronze from Saturday.
Kenny was pipped out of top spot on the podium by Germany's Maximilian Levy while fellow Brit Matthew Crampton was eighth in the same event.
In the women's keirin double world champion Becky James had to settle for seventh while her team-mate Victoria Williamson was ninth.