Two bidders battled it out for the work before the hammer finally came down, triggering a round of applause at the Sotheby's auction house.
The book contains commentary and 22 of Rowling's own original illustrations.
The lot formed part of a sale of books annotated by 50 British and Commonwealth contemporary writers, raising a combined total of £439,200.
The second-highest price was achieved for another children's classic, Roald Dahl's Matilda, which sold for £30,000.
Other lots auctioned included works by Julian Barnes, Alan Bennett, Seamus Heaney and Hilary Mantel.
Many authors represented at the sale turned up in person, including Helen Fielding, Frederick Forsyth and Ben Okri.
"This is a triumphant conclusion to a wonderful project, which has involved the hard work and good will of so many people," said Rick Gekoski, who curated the collection for sale.
"I am sure that the buyers of the individual books will be thrilled with their purchases," he added.