The fine was announced at Stafford Crown Court, central England, after Merlin admitted breaching health and safety rules over the accident on "The Smiler" ride.
Two victims of the crash required leg amputations.
Merlin, the world's second-biggest visitor attractions group behind Walt Disney, pleaded guilty to the breach at an April hearing.
The firm said in November its own investigation concluded the crash was caused by human error. It found the manual override of the ride safety control system was implemented without appropriate protocols being followed.
Merlin's trade at Alton Towers has suffered since the crash, with the firm predicting a two-year period before visitor numbers recover fully.
However, shares in the firm have increased 26 percent over the last year, reflecting robust trade in other parts of the business. They were up 0.8 per cent at 466.6 pence at 10.48 GMT.