Agriculture Minister John MacDonell says the merger is intended to strengthen the college, which has experienced financial problems in recent years.
The college was one of six identified in a 2010 report by consultant Tim O'Neill as being at risk because of financial challenges that could threaten its long-term viability.
At the time, O'Neill said it was one of four potential candidates for a merger.
Under the agreement, college faculty and staff will become Dalhousie employees.
The merger takes effect July 1.
The Nova Scotia Agricultural College employs about 300 faculty and staff and has an enrolment of about 1,000 students.
It was founded in 1905.