Suzuki, who held an eight-point lead over Asada after the short program, made several mistakes in the final but scored 119.43 points for a total of 185.98, just 1.79 points ahead of Asada.
"I'm very happy to have won my first NHK Trophy but I'm not at all satisfied with my free skate," Suzuki said. "I will reflect on my mistakes and try to improve them."
Russian skater Alena Leonova was third with 170.68 points. Ashley Wagner of the United States finished fourth with 165.55 points.
As she did in the short program, Asada's failure to hit a triple axel on her opening element cost her valuable points. She tried the triple again Saturday but only managed a double.
"I cleared my own goals, except for the triple axel," said Asada. "I skated my other elements well. I'm not yet at the level I want to be. I can level up."
Suzuki, skating to "Die Fledermaus" did a single lutz instead of a planned triple lutz later in her routine and singled a triple loop but her lead from the short program was big enough to secure the win.
It was Suzuki's first victory at the senior grand prix series since the 2009 Cup of China. Her victory here, coupled with a second-place finish as Skate Canada, qualified her for the Dec. 8-11 Grand Final in Quebec City, Canada.The Nov. 11-13 NHK Trophy is the fourth event of the 2011 International Skating Union's Grand Prix series.
In the men's short program, Vancouver bronze medalist Daisuke Takahashi of Japan finished first, hitting all his jumps to score a personal-best 90.43 points. Takahiko Kozuka, also of Japan, was second with 79.77 points.
Brandon Mroz of the United States, who placed third with 74.83 points, made skating history by becoming the first skater to land a quadruple lutz in international competition.
The 20-year-old Mroz hit the quadruple lutz on his opening jump.
"I'm excited to get it done in an international competition," Mroz. "Getting another jump done is awesome for generations of skaters to come."
Mroz previously made the quadruple lutz on Sept. 16 at the Colorado Spring Invitational, a U.S Figure Skating sanctioned event.
In the ice dance, Maia and Alex Shibutani of the United States rallied from third place to win their first grand prix title.
The Japanese-American pair received a personal-best 92.83 points in the free dance to capture their first senior grand prix title with a total of 151.85 points.
"After the short dance, we felt pretty confident going into today's program," Alex Shibutani said. "It's great to get our first grand prix title here in Japan where the fans really support us."
Kaitlyn Weaver and Andrew Poje of Canada were second with 151.76 points while Russians Elena Ilinykh and Nikita Katsalapov, first after the short dance, took the bronze medal with 149.48 points.
The Shibutanis won the bronze medal at the 2011 world championships. Their previous best result at a grand prix event was second place at last week's Cup of China in Shanghai.
Lynn Kriengkairut and Logan Giulietti-Schmitt of the United States collided with Cathy Reed and Chris Reed of Japan in the warm-up but both couples were able to perform their routines and finished sixth and seventh, respectively.
In the pairs final, Yuko Kawaguchi and Alexander Smirnov of Russia won the gold medal after receiving 122.49 points in the free skate. The Russian pair were fifth after the short program but impressed the judges with near-flawless performance to finish with 177.51 points.
Narumi Takahashi and Mervin Tran of Japan were second with 172.09 points while world champions Aliona Savchenko and Robin Szolkowy of Germany finished third with 171.68 points.