Rice had hoped to sign the agreement on a visit to New Delhi a week ago, just after the accord was approved by the U.S. Congress.
But bureaucratic snags prevented a signing at that time, and Foreign Minister Mukherjee flew to Washington Friday to formally conclude an agreement both sides call historic.
Three years in the making, the agreement will give India access to U.S. nuclear fuel, reactors and technology, overturning a ban on such trade imposed after India's first nuclear test in 1974.
The agreement was controversial in both capitals with U.S. critics saying it weakens U.S. non-proliferation policy.
Indian opponents - who nearly brought down Prime Minister Monmohan Singh's government earlier this year - say it could limit the country's nuclear weapons program.
But at the signing ceremony, Secretary Rice said the accord puts an end to decades of distrust between the two countries and opens the door to vastly expanded cooperation far beyond the nuclear field. "India and the United States can do all of this and more together. There is so much that our two great nations will achieve in this century, and with conclusion of this civil nuclear agreement, our partnership will be limited only by our will and our imagination. India and the United States have taken on an extremely difficult challenge. We've met it, we've succeeded together," she said.
Foreign Minister Mukherjee for his part said India looks forward to working with U.S. companies eager to enter India's potential multi-billion dollar nuclear market. He said expanded civil nuclear power is central to the country's hopes for enviromentally safe economic growth.
"Nuclear power will directly boost industrial growth, rural development, and help us respond in every vital sector in our economy. It will also enable India to respond with our global partners to the challenges of climate and global warming, by strengthening her economic growth and sustainable development," he said.
President Bush earlier this week signed into law enabling legislation for the nuclear deal approved by the U.S. Congress.
It clears the way for U.S. nuclear assistance in exchange for India's agreement to open civilian, but not military, nuclear facilities to international inspection.
Casting the accord as a major foreign policy achievement, Bush administration officials say the partial opening of Indian nuclear facilities to outside scrutiny is a significant advance.
Opponents in U.S. arms control groups say rewarding India, which has refused to sign the Nuclear Non-Proliferation Treaty, is a poor example at a time when the world community is trying to get Iran and North Korea to curb their nuclear programs.