The French, Scottish and Dutch scientists had developed molecules with controllable movements that can perform tasks when energy is added, the Academy said in a statement awarding the 8 million Swedish crown (US$931,000) prize.
Sauvage is professor emeritus at the University of Strasbourg and director of research emeritus at France's National Center for Scientific Research.
Stoddart, born in Edinburgh, is professor of chemistry at Northwestern University in the United States, while Feringa is professor in organic chemistry at the University of Groningen in the Netherlands.
Chemistry is the third of this year's Nobel prizes after the medicine and physics laureates were announced on Monday and Tuesday.