The 2016 crash raised questions about the tuk-tuk's design and certification.
According to the NZTA investigation, Joyce did not view the Auckland tuk-tuks before signing their certificates. NZTA subsequently complained to Engineering New Zealand.
Engineering New Zealand's disciplinary committee determined the structural strength of the tuk-tuks was insufficient to provide reasonable protection for the occupants.
"The certification of vehicles for passenger service is a safety-critical task, and members of the public rightly rely on regulators such as NZTA to protect them from harm," the committee's decision said.
"Regulators, in turn, rely upon experts including professional engineers to carry out their role competently.
"Mr Joyce has departed from what could be expected of a reasonable engineer, and this departure is serious."
Engineering New Zealand upheld the complaint and suspended Joyce's membership.
His suspension will continue for three years, starting from February. During this period of suspension, Joyce must fulfil requirements for professional development specified by the committee before he can be considered for readmission as a member.
Joyce must also pay $15,000 towards the costs incurred by Engineering New Zealand in investigating his conduct.
"There needs to be a measure of public protection in our orders while also recognising that there is potential for Mr Joyce to learn from this matter and rehabilitate," the decision said.
"In making this order, we are mindful that an engineer suspended from membership is deprived of the peer support and other collegial aspects of belonging to a professional body, but we are of the view that this consideration is outweighed by the need to protect the public."