The trio, who all work at US universities, were honoured for "their discoveries of machinery regulating vesicle traffic, a major transport system in our cells," it said.
Their discoveries have had a major impact on understanding how cargo is delivered within and outside the cell and have implications for work on several diseases including neurological and immunological disorders, as well as diabetes, the Nobel committee said.
Each cell is a factory that produces and exports molecules.
"For instance, insulin is manufactured and released into the blood and chemical signals called neurotransmitters are sent from one nerve cell to another. These molecules are transported around the cell in small packages called vesicles," it explained.
The three Nobel laureates "have discovered the molecular principles that govern how this cargo is delivered to the right place at the right time in the cell," it said.
The winners will share equally the prize sum of eight million Swedish kronor ($1.25 million, €925,000), reduced because of the economic crisis last year from the 10 million kronor awarded since 2001.
Last year, the honour went to Shinya Yamanaka of Japan and John Gurdon of Britain for their work on cell programming, a frontier that has raised dreams of replacement tissue for people crippled by disease.
In line with tradition, the laureates will receive their prize at a formal ceremony in Stockholm on December 10, the anniversary of prize founder Alfred Nobel's death in 1896.