Jean-Pierre Sauvage, Sir J Fraser Stoddart and Bernard L Feringa will share the 8m kronor (€ 824 000) prize for the design and synthesis of machines on a molecular scale.
They were named at a press conference in Sweden.
The machines conceived by today's laureates are a thousand times thinner than a strand of hair.
They could slip inside the human body to deliver drugs from within - for instance, applying pharmaceuticals directly to cancer cells.
This field of nanotechnology could also yield applications in the design of smart materials.
The prize recognises their success in linking molecules together to design everything from motors to a car and muscles on a tiny scale.
"They have mastered motion control at the molecular scale," said Olof Ramström, from the Nobel Committee.
Reacting to the award, Prof Feringa said: "I don't know what to say, I'm shocked. And my second remark was: 'I'm a bit emotional about it'."
The celebrated physicist Richard Feynman is often credited with inspiring the concept of molecular machines.
In a lecture at the California Institute of Technology (Caltech) in 1959, titled "There's plenty of room at the bottom", he considered the possibility of the direct manipulation of matter at the atomic scale.
He talked about the idea of "swallowing the doctor" - introducing the drug delivery concept.
Jean-Pierre Sauvage was born in 1944 in Paris, France. He is currently emeritus professor at the University of Strasbourg and director of research emeritus at the French National Center for Scientific Research (CNRS).
His work provided early breakthroughs in the area of molecular machines. He had been researching the use of sunlight to drive chemical reactions but this work helped him work out that he could link different molecules together in a chain.
This was the first step towards building molecular machines. In 1994, Prof Sauvage's research group succeeded in making one molecule rotate around the other in a controlled manner when energy was applied.
Sir Fraser Stoddart was born in 1942 in Edinburgh, UK. He is currently affiliated to the Northwestern University, in the US.
The Briton made a key advance by threading a molecular ring on to a rod-like structure that acted as an axle.
Sir Fraser then made use of the ring's freedom to move along the axle. When he added heat, the ring jumped forwards and backwards - like a tiny shuttle.
His group later built on this discovery to build numerous molecular machines, including a lift, a muscle and - in partnership with other researchers - a computer chip.
Bernard Feringa was born in 1951 in Barger-Compascuum, in the Netherlands. He is a professor in organic chemistry at the University of Gröningen, the Netherlands.
In 1999, Prof Feringa led the first research to produce a molecular motor that continually spins in the same direction.
"I feel a little bit like the Wright Brothers who were flying 100 years ago for the first time and people were saying why do we need a flying machine and now we have a Boeing 747 and an Airbus," said Bernard Feringa.
"The opportunities are great."