Here are twelve influential books covering the history of science and mathematics. All of them have changed the world in some way:
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1: Euclid’s Elements (c. 300 BC). Possibly the most influential mathematics book ever written, and used as a textbook for more than 2,000 years.
2: De rerum natura by Lucretius (c. 50 BC). An Epicurean, atomistic view of the universe, expressed as a lengthy poem.
3: The Vienna Dioscurides (c. 510 AD). Based on earlier Greek works, this illustrated guide to botany continued to have an influence for centuries after it was written.
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5: Galileo’s Dialogue Concerning the Two Chief World Systems (1632). The brilliant sales pitch for the idea that the Earth goes around the Sun.
8: Beilstein’s Handbook of Organic Chemistry (1881). Still (revised, in digital form) the definitive reference work in organic chemistry.
9: Relativity: The Special and the General Theory by Albert Einstein (1916). An explanation of relativity by the man himself.
10: Éléments de mathématique by “Nicolas Bourbaki” (1935 onwards). A reworking of mathematics which gave us words like “injective.”
11: Algorithms + Data Structures = Programs by Niklaus Wirth (1976). One of the early influential books on structured programming.
12: Introduction to VLSI Systems by Carver Mead and Lynn Conway (1980). The book which revolutionised silicon chip design.
That’s four books of biology, four of other science, two of mathematics, and two of modern IT. I welcome any suggestions for other books I should have included.
Scientific Gems 
Philosophiæ Naturalis Principia Mathematica?
Good call. I thought of listing that, but I only wanted one physics book for the period, so I opted for Galileo, who was also very influential.