Dungeon Siege has also done well, shifting 820,000 units.
Eidos Montreal's Deus Ex prequel, Human Revolution, has sold 2.18m copies since its launch on September 30, Square Enix has reported.
Human Revolution sold 800,000 copies in North America and 1.38m in Europe, according to the publisher's mid-year financial report.
The well-received Dungeon Siege 3 has shifted 820,000 units, of which 480,000 were bought in Europe.
Another figure of note reveals that Square Enix has made ¥4.6 billon (£36.8m) from its web, social networking and smartphone content over the past 18 months.
Square Enix's net sales totalled ¥57.5bn over the six months between April and September this year, a 16 per cent drop from the same period in 2010. Net profits increased 118 per cent year-on-year, however.