Charles Darwin's monumental formulation of the theory of evolution has been overwhelmingly voted as the most influential and important academic book, ahead of works by Newton, Plato and Einstein.
"Thus, from the war of nature, from famine and death, the most exalted object which we are capable of conceiving, namely, the production of the higher animals, directly follows. There is grandeur in this view of life, with its several powers, having been originally breathed by the Creator into a few forms or into one; and that, whilst this planet has gone circling on according to the fixed law of gravity, from so simple a beginning endless forms most beautiful and most wonderful have been, and are being evolved."
Now that's how you write a book! Darwin's book came out November 1859, basically defining how we think of biology for the next 150 years. But it wasn't this popular in the beginning. The book aroused massive interest, but also controversy and criticism. Much of the initial reaction was hostile, but Darwin had to be taken seriously as a prominent and respected name in science. There was much less controversy than had greeted the 1844 publication Vestiges of Creation, which had been rejected by scientists, but had influenced a wide public readership into believing that nature and human society were governed by natural laws, Darwin's book legitimised scientific discussion of evolutionary mechanisms, and the newly coined term Darwinism was used as an umbrella term for many other ideas, not just his own.
But now, looking back on it, there's no denying its influence; it changed not only how we think about biology and other animals, but also how we think about ourselves. Professor Andrew Prescott of the University of Glasgow called Darwin’s 1859 study "the supreme demonstration of why academic books matter," saying:
“Darwin used meticulous observation of the world around us, combined with protracted and profound reflection, to create a book which has changed the way we think about everything – not only the natural world, but religion, history and society,” he said. “Every researcher, no matter whether they are writing books, creating digital products or producing artworks, aspires to produce something as significant in the history of thought as Origin of Species.”
But Darwin's book also played another crucial role: it showed that in a time when already papers and journals were regarded as the scientific standard, academic books are still very important. Personally, I feel like it's not really possible to distinguish, in terms of importance, between (for example) Darwin's book and Newton's Philosophiae Naturalis Principia Mathematica, so while it's important to acknowledge the importance of academic books, it's maybe not that relevant to classify them.
But, even so, here is the rest of the top, as seen by expert academic booksellers, librarians and publishers:
A Brief History of Time by Stephen Hawking
A Vindication of the Rights of Woman by Mary Wollstonecraft
Critique of Pure Reason by Immanuel Kant
Nineteen Eighty-Four by George Orwell
On the Origin of Species by Charles Darwin
Orientalism by Edward Said
Silent Spring by Rachel Carson
The Communist Manifesto by Karl Marx and Friedrich Engels
The Complete Works of William Shakespeare
The Female Eunuch by Germaine Greer
The Making of the English Working Class by EP Thompson
The Meaning of Relativity by Albert Einstein
The Naked Ape by Desmond Morris
The Prince by Niccolò Machiavelli
The Republic by Plato
The Rights of Man by Thomas Paine
The Second Sex by Simone de Beauvoir
The Uses of Literacy by Richard Hoggart
The Wealth of Nations by Adam Smith
Ways of Seeing by John Berger