The pact has been a source of contention at home and abroad because India is neither a signatory of the Treaty on the Non-Proliferation of Nuclear Weapons (NPT) nor of the Comprehensive Nuclear Test Ban Treaty.
Opposition lawmakers argue that the accord will damage the credibility of the NPT system and help India acquire nuclear technology and materials.
Signed by Prime Minister Shinzo Abe and his Indian counterpart Narendra Modi in November last year, the agreement passed a plenary session of the Upper House Wednesday with a vote of 151 to 87.