The measure will come into place on Tuesday, authorities announced.
With 46 new cases registered on Thursday, the figures are worrying, said regional health chief Mauro Poggia on Friday.
Poggia said the situation was worsening and stricter measures needed to be taken.
Geneva is following in the footsteps of the cantons of Vaud and the Jura, which have already introduced a similar rule.
Shoppers will also be forced to disinfect their hands with hydro-alcoholic solution before entering the store. `
Authorities in Geneva also announced that wearing masks will be compulsory for all those who work in beauty and therapy industry, including hairdressers.
The rise in cases in the area has been blamed on a general slacking off of members of the pubic with regards to social distancing and hygiene rules as well as young people returning to bars and holding private parties.
From Friday night bars and discos were obliged to collect the identity and a reliable means of contact for each client.
Venues that don't comply risk steep fines.
Staff at pubs and restaurants must also be masked. These measures will remain in place until at least October.