Serge Haroche of France and David Wineland of the US will share the prize, worth 8m Swedish krona (£750,000; $1.2m).
Their work deals with single photons and ions, the basic units of light and matter.
It could lead to advanced modes of communication and computation.
The Nobel citation said the award was for "ground-breaking experimental methods that enable measuring and manipulation of individual quantum systems".
Working with light and matter on this level would have been unthinkable before the pair developed solutions to pick, manipulate and measure photons and ions individually, allowing an insight into a microscopic world that was once just the province of scientific theory.
Prof Haroche was reached by phone from the press conference. He had been told he had won just 20 minutes before telling reporters: "I was lucky - I was in the steet and passing near a bench, so I was able to sit down immediately.
"I was walking with my wife going back home and when I saw the... Swedish code, I realised it was real and it's, you know, really overwhelming."
The Nobel prizes have been given out annually since 1901, covering the fields of medicine, physics, chemistry, literature, peace and economics.
The first-ever Nobel prize in physics was awarded to Wilhelm Roentgen of Germany for his discovery of X-rays, and with this year's winners the total number of recipients has reached 194.
On Monday, the 2012 prize for medicine or physiology was awarded to John Gurdon from the UK and Shinya Yamanaka from Japan for changing adult cells into stem cells, which can become any other type of cell in the body.
This year's chemistry prize will be announced on Wednesday, with the literature and peace prizes to be awarded later in the week.
source: BBC
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