She just got up to score on the line after a battle for the last 100m with Jaguar Mail taking third in a race where the home team filled each of the first five places.
Buena Vista was breaking a long drought, having failed to win since last year's Japan Cup, when she was controversially thrown out for interference under Christophe Soumillon.
Rose Kingdom, who was awarded last year's race, was only ninth yesterday, but there was to be no redemption for Soumillon.
He partnered the John Hammond-trained Sarah Lynx to finish 12th of the 16 runners, one place ahead of Dubai World Cup winner Victoire Pisa, adrift of the remainder for much of the race on his comeback after injury.
The winning trainer, Hiroyushi Matsuda, said he had never lost faith in Buena Vista, now set to run in the Arima Kinen, the end-of-season championship on December 25. There is no decision on a possible overseas campaign at the start of 2012.
"I was never in doubt about her ability during this season, even in defeat - she has always maintained her form," said Matsuda.
"She proved that she could keep up with the high pace in the Tenno Sho Autumn and secure a fourth place while still not in her best form - it gave me even more confidence in her.
"Her age has only been a plus for us in that she can settle better and be easier to handle.
"I felt sorry for Christophe Soumillon because of the unfortunate demotion despite their convincing performance last year, and it means a lot to me that we were able to get our revenge this time."
Jockey Yasunari Iwata was a relieved man after a frustrating 2011 campaign for Japan's favourite horse. "I was determined to show that Buena Vista is really the very best in Japan. I just kept believing in her exceptional power while duelling with Tosen Jordan at the stretch and urged her on, to which she really responded well.
"It's a great feeling to have been able to give her the well-deserved Japan Cup title."
Iwata is well known in the Southern Hemisphere as the rider of 2007 Melbourne Cup winner Delta Blues.
From her wide draw, Arc winner Danedream was forced to race towards the rear of the main body of the field.
She closed well in the straight but had too much to do and finished sixth, about 3 lengths behind the winner. In a few more strides, she might have got third but much of the damage had been done in the early stages and she was never going to catch the principals.
"Breaking from a wide stall took a lot out of her," said trainer Peter Schiergen. "It was difficult for her to find a comfortable position on a fast track and that showed in the outcome."
