The 20-year-old Olympic and world champion followed on from her team pursuit success with Dani King and Elinor Barker on Friday in the six-discipline event at the Sir Chris Hoy Velodrome.
Trott needed to beat Australian Ashlee Ankundinoff by two clear places in the 500m time trial to take the victory and she finished second while her rival had to settle for fourth.
Both finished with 24 points but the 20-year-old from Essex triumphed on countback after winning both the elimination race and the individual pursuit.
Russia's Tamara Balabolina was third.
The hosts finished with three golds and six medals in total for the weekend.
Steffan Boetticher beat German compatriot Robert Forstemann to win the men's sprint. Denis Dmitriev took bronze.
Philip Hindes lost his last 16 match against Pavel Keleman while fellow Brits Jason Kenny and Lewis Oliva did not compete after crashes in the keirin.
Another German Kristina Vogel won the women's keirin ahead of Russia's Ekaterina Gnidenko and Wai Sze Lee of Hong Kong.
Becky James finished fifth for Great Britain while in her fourth discipline, Jess Varnish was third in the B final.