Jaguar Mail finished third and Victoire Pisa, winner of the Dubai World Cup, was 13th in his first start since that March event.
Of the four foreign-based runners, the best finish was by Danedream, winner of the Prix de l'Arc de Triomphe, who went to the post as the favorite but finished sixth. Shareta, second in the Arc, was seventh. Sarah Lynx finished 12th and U.S. runner Mission Approved got home 14th.
A year ago, Buena Vista was Japan's super horse. Then, she was disqualified from an apparent victory in the 2010 Japan Cup and had not won since. She finished fourth in the Autumn Tenno Sho in her last previous outing, causing some fans to think she had lost her ability at the highest level.
Not so trainer Hiroyoshi Matsuda.
"I knew she was the best. I always believed in her," the 65-year-old Matsuda said after Sunday's big race. "She had not been 100 percent in the Tenno Sho and had trouble under way. Then with the fast pace. To have come forth in those conditions just gave me more confidence in her ability."
After breaking well from the No. 2 post, jockey Yasunari Iwata kept Buena Vista on the rail in the second flight while Mission Approved dictated at a slow pace. Into the stretch, Iwata brought the 5-year-old mare out through some traffic, then broke through the pack to run alongside Tosen Jordan before pulling away for the win.
"She had felt fantastic the whole way around," Iwata said. "I believed she was the strongest to the end and she had enough to pull out ahead."
Still, he described the Tokyo Race Course stretch as "endless."
Buena Vista ran the final 3 furlongs in 33.9 seconds and finished the 2,400 meters of firm turf in 2:24.2.