The winners are British scientist Michael Houghton and US researchers Harvey Alter and Charles Rice.
The Nobel Prize committee said their discoveries ultimately "saved millions of lives".
The virus is a common cause of liver cancer and a major reason why people need a liver transplant.
In the 1960s, there was huge concern that people receiving donated blood were getting chronic hepatitis (liver inflammation) from an unknown, mysterious disease.
The Nobel Prize committee said a blood transfusion at the time was like "Russian roulette".
Highly sensitive blood tests mean such cases have now been eliminated in many parts of the world, and effective anti-viral drugs have also been developed.
"For the first time in history, the disease can now be cured, raising hopes of eradicating Hepatitis C virus from the world," the prize committee said.
However, the virus still infects 70 million people at year and kills around 400,000.