The Harry Potter novelist published the book - The Cuckoo's Calling - as Robert Galbraith.
The book had sold fewer than 500 copies before the secret emerged in the Sunday Times, according to Nielsen BookScan's figures.
Within hours, it rose more than 5,000 places to top Amazon's sales list.
The digital version is now also at number one in the iTunes book chart.
The book was published by Sphere, part of Little, Brown Book Group which published Rowling's first foray into writing novels for adults, The Casual Vacancy.
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Little, Brown's David Shelley confirmed to The Bookseller the publisher had ordered an "immediate reprint" with the number not yet confirmed.
Rowling said she had "hoped to keep this secret a little longer".
The author described "being Robert Galbraith" as "such a liberating experience".
A spokesman for bookseller Waterstones said: "This is the best act of literary deception since Stephen King was outed as Richard Bachman back in the 1980s."
One reviewer described The Cuckoo's Calling as a "scintillating debut", while another praised the male author's ability to describe women's clothes.
Crime writer Peter James told the Sunday Times: "I thought it was by a very mature writer, and not a first-timer."
Fellow crime author Mark Billingham, who reviewed the book ahead of its publication in April, said he was "gobsmacked" at the revelation.
The fictitious Galbraith was supposed to have been a former plain-clothes Royal Military Police investigator who had left the armed forces in 2003 to work in the civilian security industry.
However a clue that Rowling was behind the novel was that she and Galbraith shared an agent and editor.
In previous interviews, Rowling has said she would prefer to write novels after Harry Potter under a pseudonym.
Another Cormoran Strike book by Robert Galbraith is in the pipeline, to be published next year.
JK Rowling's "secret" crime novel has topped book charts after it was revealed she had written it under a pseudonym.