Wise edged countryman Torin Yater-Wallace by only .2 points, 93.8 to 93.6. France's Kevin Rolland was breathing down Wise's neck, too, finishing third with a score of 93.0.
Wise's winning score came on his first run, which was the same as the one he used to win a gold medal at the X Games this year.
"It's kind of my statement run of the year - back-to-back-to-back double corks," he said. "It's one of the more innovative runs we've seen in halfpipe and my way of saying, 'This is what I like about skiing.'"
However, he fell on his second run and had to wait at the bottom of the pipe to see if his first-run score would hold up.
"I had to watch all the best guys in the world drop in after me," Wise said. "That was pretty nerve-wracking, but exciting. That's what the sport is all about."
Bowman, who is living and training in Park City and attending school at Westminster College, had a slightly bigger cushion over the second-place finisher in the women's finals, defeating Japan's Ayana Onozuka 85.2 to 84.4. Switzerland's Virginie Faivre finished third with a score of 82.8.
Bowman said she would have liked to have scored higher, but was happy with the win.
"I wish it would have been a little cleaner or bigger," she said. "I just want to do better.
She added that conditions were nearly perfect for the competition at PCMR, leading to more daring runs from some of the competitors.
"This is the first warm, soft pipe we've gotten to ski in. It's nice; I feel like I'm home in California," she said. "When it's warmer we feel more comfortable and we're not as afraid to throw those bigger tricks."
Of course, bigger tricks often mean bigger falls. Five of the 12 men's finalists fell during the event, in addition to several women.
Skier Simon D'Artois of Canada crashed on his first run of the finals, hitting his head on the edge of the pipe and losing consciousness. He was airlifted from the pipe and diagnosed with a concussion, but is expected to make a full recovery.
After the X Games, Bowman and Wise will be competing for spots on the Olympic team. The 2014 Winter Olympics in Sochi, Russia, will feature the first-ever Olympic ski halfpipe competition.
But Bowman said she's trying to relax and not worry about the future.
"I try not to think about the Olympics too much," she said. "I'm just trying to have fun and not put too much pressure on myself."
After this past weekend's competition, Bowman is looking forward to some much-needed rest.
"I'm ready for a little break," she said.