"Many thought this day would never come, but doubts have been silenced," Rice said just before she and Mukherjee signed the document in Washington.
Before he signed the pact, Mukherjee alluded to the business opportunities that may await US firms, saying: "We look forward to working with the US companies on the commercial [steps] that will follow to implement this landmark agreement."
The agreement offers India access to US technology and cheap atomic energy in return for allowing UN inspections of some of its civilian nuclear facilities - but not military nuclear sites.
George Bush, the US president, signed legislation to enact the landmark agreement on Wednesday.
Bush and Manmohan Singh, the Indian prime minister, signed the deal in July 2005, sparking controversy within both nations' governments.
Those opposed to the deal say it undermines efforts to curb nuclear proliferation and could trigger an arms race in South Asia, particularly with Pakistan, India's nuclear armed neighbour.