"I am pleased that our two countries will soon have increased opportunities to work together to meet our energy needs in a manner that does not increase air pollution and greenhouse gas emissions, promotes clean development, supports nonproliferation and advances our trade interests," Bush said in a statement.
"I appreciate Congress's support for the US-India civil nuclear cooperation initiative," Bush said, adding: "I look forward to signing this bill into law soon."
The US Senate passed the deal by voice vote early Saturday, after an all-night session. The House of Representatives approved it 330-59 late Friday.
The legislation reconciles separate bills adopted by the House and Senate aimed at implementing a nuclear agreement between Bush and Indian Prime Minister Manmohan Singh in July of last year.
Under the controversial deal, India, a non-signatory of the nuclear Non-Proliferation Treaty (NPT), will be given access to civilian nuclear fuel and technology in return for placing its atomic reactors under global scrutiny.
The US Congress had to create a rare exception for India from some of the requirements of the US Atomic Energy Act, which currently prohibits nuclear sales to non-NPT signatories.
Washington halted nuclear cooperation with India after it conducted its first nuclear test in 1974.