The petition filed by businessman Enock Aura said the directive, which was to be implemented next week, was unconstitutional and discriminatory.
High Court Judge Anthony Mirima said his ruling would remain in force until the case was heard on 4 January 2022 and until a decision made.
In November, Health Minister Mutahi Kagwe said that the directive was aimed at getting more Kenyans to get the jab.
The government had set a target of vaccinating 10 million Kenyans by the end of the year.
Only 8.1 million people have received a Covid-19 vaccine and more than three million have received a two doses.
The suspension of the directive also comes days after a number of hotels and malls announced that they would not allow unvaccinated Kenyans into their premises.