Trott, who won round two in Glasgow but was not competing in Aguascalientes, won Olympic gold ahead of Hammer at the London Games last summer.
But the American exacted revenge of sorts by taking victory on the night and with it the overall World Cup title.
World junior time trial champion Elinor Barker moved up two places, finishing 15th in Mexico.
Team USN rider Barker, who collected team pursuit bronze with Amy Roberts and Ciara Horne on day one in a new personal best, began the final three omnium events ranked 17th overall.
However ninth in the individual pursuit in 3:39.016, 15th in the scratch race and a time of 36.878 in the 500m TT saw her move up two places.
Meanwhile, Russia's Denis Dmitriev helped bring the curtain down on the third and final meeting with victory in the men’s sprint.
Dmitriev fell short of breaking Kevin Sireau’s world record of 9.572 for the 200m flying start, but his victory in the final brought him the overall sprint title.
Meanwhile George Atkins made his debut for Team USN in the Madison with Jon Mould, who had to pull out of the men's omnium after four events because of illness.
The British champions, who were both recovering from being sick, started well and picked up an early sprint point, before finishing 13th as French duo Vivien Brisse and Thomas Boudat took the win. They beat the Ukrainian duo of Mykhaylo Radionov and Sergiy Lagkuti to gold and Switzerland took the bronze medal.
And China dominated the women's keirin, registering a one-two-three with Zhong, Jinjie Gong and Yulei Xu on the podium.
Germany's consistent performances throughout the three meetings - in Cali, Glasgow and Aguascalientes - brought them the overall team title.