Aliens: Colonial Marines sold just over 1.3 million units during Sega's fiscal year ended March 31.
It was the publisher's second best-performing title behind Sonic & All-Stars Racing Transformed, which released on more platforms and managed to beat the critically panned shooter by 50,000 units.
Sales in Sega's consumer business, which houses games, were down 2.1 per cent year-on-year to 83.8 billion yen (£536m).
Sega parent Sega Sammy said: "In the home video game software industry, demand weakened for packaged games due to the severe economic environment mainly in the US and Europe.
"Meanwhile, Sega Sammy Group needs to adapt to a changing business environment in which market demand for digital games geared toward social networking services (SNS) and smartphones is expanding further.
"The packaged game software field in the consumer business will undergo rationalization, in an effort to establish a structure that can consistently generate profit. We also intend to make our game software compatible with the next-generation game machines, which are due to be launched."
Sega Sammy's net sales fell 18.7 per cent year-on-year to 321 billion yen (£2b), while net income increased 53.3 per cent to 33.5 billion yen (£214m).