The DB10, one of only two "show cars" from the 10 made specially for the film, smashed its reserve price of £1m.
Made in Warwickshire, the model has a 4.7-litre V8 petrol engine and a top speed of 190 mph - but it cannot be driven on public roads.
"Spectre - The Auction", at Christie's London King Street, saw 10 lots raise £2,785,500 for charities.
A further 14 items continue in an online auction which ends next Tuesday.
Other lots included the "Day of the Dead" costume worn by Daniel Craig in Spectre, which sold for £98,500.
Sam Smith's Writing on the Wall record and sheet music went for £9,375.
Aston Martin has been associated with Bond since the 1964 film Goldfinger, which featured a DB5.
The auctioned DB10, hand built at Aston Martin's UK headquarters in Gaydon, was signed by Daniel Craig.
Most of the DB10s were modified for use in the filming of Spectre but two were left unmodified for display.
The film is reported to have destroyed $36m (£25m) worth of cars during shooting.
An Aston Martin sports car from the James Bond film Spectre has sold at auction for £2,434,500.