Jacques Dubochet of Switzerland, Joachim Frank of the US and Richard Henderson of the UK were awarded the prize for cryo-electron microsopy.
The technique allows scientists to freeze biomolecules in action and "visualise processes they have never previously seen," according to the Nobel statement.
The method means that, for example, molecules in bacteria and viruses -- such as the Zika virus -- can be examined under a microscope in their native, undamaged state.
This development is "decisive for both the basic understanding of life's chemistry" and the development of drugs, the Nobel committee said.
The announcement was made Wednesday in Stockholm.
"We are facing a revolution in biochemistry," said Nobel Committee Chairman Sara Snogerup Linseduring the announcement. "Now we can see the intricate details of the biomolecules in every corner of our cells, in every drop of our body fluids. We can understand how they are built and how they act and how they work together in large communities."
"Soon there are no more secrets," she said.
'Immense' practical use
Until now, scientists have been unable to produce detailed images of many biological molecules that are the building blocks of life.
Previous techniques often required the use of dyes or fixatives to help see these molecules. In the past, electron microscopes were also assumed to be useful only in imaging dead material due to electron beams destroying biological matter.
Now, with the development of cryo-electron microscopy, researchers can freeze biomolecules mid-movement and observe how they act -- and interact.
Speaking at the conference by telephone, Frank said that the development of cryo-electron microscopy "fills an important gap and extends the range of molecules that can be determined at atomic resolution."
He described the practical uses of the technique as "immense" but said that it would take several years before the implications would be fully understood.
Frank was born in Germany in 1940 and is now a professor at Columbia University in New York.
His Swiss colleague Dubochet was born in 1942 and is honorary professor of biophysics at the University of Lausanne in Switzerland.
The third recipient, Richard Henderson, was born in Scotland in 1945 and works at the MRC Laboratory of Molecular Biology in Cambridge, England.
Initial reactions from the academic community of chemists have been positive.
John Hardy, professor of neuroscience at University College London, described the development of cryo-electron microscopy as "transformative."
"To give one example, last year the 3D structure of the enzyme producing the amyloid(protein) of Alzheimer's disease was published using this technology," Hardy said. "Knowing this structure opens up the possibility of rational drug design in this area."
"A visual image is the essential component to understanding," said Magdalena Zernicka-Goetz,professor of mammalian development and stem-cell biologyat the University of Cambridge. Such an image is often the...
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