Members of parliament on both the majority and minority sides backed the approval.
The 38-year-old medical professional was nominated as Deputy Minister earlier this month by President Akufo-Addo.
His appointment by President Akufo-Addo has become crucial as Ghana battles the deadly Coronavirus pandemic.
He replaces Alexander Kodwo Kom Abban, who has been reassigned to the Communication Ministry as a Deputy Minister.
The Appointment Committee vetted him on Wednesday, after which parliament was recalled from suspension to approve his nomination.
Speaker of Parliament Prof. Mike Oquaye congratulated Dr Okoe-Boye after the House approved his appointment.