The Japanese was second after the short programme but her total of 181.76 was 3.84 points better than Lipnitskaia as she claimed the seventh Grand Prix title of her career.
The Russian dominated the junior scene last year and won on her senior international debut in Finland but she was unable repeat the trick on her Grand Prix bow in Shanghai after an error-strewn performance.
She failed to complete her opening two combinations and had to settle for silver ahead of European silver medallist Kiira Korpi (169.86).
2010 world champion Daisuke Takahashi was beaten on his season debut in the men's event.
Takahashi lost his short programme advantage to fellow Japanese Tatsuki Machida whose final total of 236.92 was 5.17 points better.
Skate America bronze medallist Machida took advantage of free programme mistakes from Takahashi to take the victory.
European champions Nathalie Pechalat and Fabian Bourzat completed a comfortable victory in the ice dance.
The French couple finished 5.44 points ahead of Russians Ekaterina Bobrova and Dmitri Soloviev who were also second at Skate America last month.
And in the pairs short program Qing Pang and Jian Tong gave the home crowd plenty to shout about as they completed victory.
The Olympic silver medallists scored 120.25 with Russians Yuko Kavaguti and Alexander Smirnov being bumped down into second on 119.83.