The award of the record came amid the first anniversary of the spacecraft's successful homecoming in June last year.
The unmanned probe was launched by the Japan Aerospace Exploration Agency (JAXA) to asteroid Itokawa in 2003, spending three months at the 500m-long potato-shaped space rock in 2005.
The main spacecraft, along with its sample-storage capsule, returned to Earth in 2010 after completing a seven-year trip spanning 6 billion km.
The probe should have come back to Earth in 2007, but a succession of technical problems delayed its return by three years.
Guinness World Records has also recognized Hayabusa as "the first spacecraft to lift off from an asteroid."