The 21-year-old from Whistler, B.C., beat out teammate Georgia Simmerling of West Vancouver, B.C., to cap off a notable season, which included gold at the Sochi Games and gold at the final World Cup race of the year to claim her second career Crystal Globe.
With Simmerling hot on her heels in the women's final, a late lunge for the line by Thompson gave her victory by the slimmest of margins.
"That was pretty exciting. I won by the length of a broken thumb," said Thompson, who tore a ligament in her thumb after crashing on a training run. "I guess you don't need thumbs for racing."
Tristan Tafel, of Canmore, Alta., took the men's race after taking the lead at the first turn to secure his second national title.
Simmerling finished in second place.
"We were neck and neck out of the gate," Simmerling said of her duel with Thompson. "I was behind her the whole way. I tried to get her at the end but I think I just missed her by a hand's length."
India Sherret, of Cranbrook, B.C., was third and veteran Danielle Sundquist, of Calgary was fourth.
The men's final was dominated by Tafel after his teammate and World Cup star Brady Leman of Calgary — who was fourth at the Sochi Games — went off course. Matt Brady and Kevin Macdonald were second and third, respectively.
"I'm pretty excited," said Tafel, who had a tough season on the World Cup circuit. "We all had a really good start and it was extremely tight going into the first turn. That's where I took the lead and kept it all the way down.
"The young guys were skiing right on my tail at the finish — good for them."
Friday's podium capped a good week for Macdonald, who won the overall Nor-Am Cup title to earn himself a World Cup spot for next season.
Macdonald topped the ski cross Nor-Am standings with 922 points, with American Robert Mahre (743) finishing second. Tania Prymak of the U.S. won the women's title with 871 points, with Canada's Abby McEwen finishing second (750).