The memoir, which includes details of the Prince’s relationship with his family – including a physical altercation with his brother, Prince William – was published in the UK by Transworld Publishers' Bantam imprint, part of Penguin Random House UK.
Some booksellers opened at midnight, with the hardback discounted at a 'half price' offer of £14.
Despite the strict security measures, apparently comparable to those surrounding the final Harry Potter books, copies were mistakenly put on sale for a few hours in Spain on 5 January.
A copy had also by then been leaked to The Guardian, sparking headlines over a fight between the two Princes that saw Harry knocked to the floor by his brother.
Running to 416 pages and weighing in at 640g, the hardback edition measures 240x160x35mm, and was both printed and bound at the UK’s largest single-site book printer, Clays.
Clays also printed the Harry Potter series of novels.
Prince Harry received a reported $20m (£16.5m) advance from Penguin Random House for a four-book deal, of which Spare is the first installation.
Penguin Random House will need to sell an estimated 1.3 million print copies worldwide and 400,000 digital editions to recoup its investment, according to Andy Lewis, former books editor of The Hollywood Reporter.
Clays employs around 750 staff at its site in Bungay, East Suffolk.
Update: Later on Tuesday, the publisher announced that it believed Spare had become the fastest-selling non-fiction book ever. Some 400,000 copies had already been sold including the hardback, ebook and audio book.