Mr Johnson also announced that the Government was taking on powers to make it more difficult for under-18s to use cigarette vending machines and may ban them if that does not work.
The move to ban prominent displays of tobacco products and advertising at the point of sale provoked storms of protest from retailers who argue it will cost them sales during the crisis.
The Tobacco Manufacturers' Association warned that the change would hit corner shops hardest as customers buy more of their cigarettes from supermarkets.
But Mr Johnson said that the ban will be introduced in supermarkets first and that corner shop owners would anyway have to "diversify" as smoking rates fall.
He said: "Any sane, rational and sensible Government will be focusing on removing what is the biggest public health risk."
Action on Smoking and Health (Ash) welcomed the announcement, although it was "disappointed" that tobacco sales would still be permitted from vending machines.
Ash director Deborah Arnott said: "The Government is to be congratulated on getting rid of these deadly displays, temptingly placed to attract children right by the sweet counter in corner shops, newsagents, supermarkets and petrol stations throughout the land.
"Claims that businesses will fail because of this measure are unfounded. In other countries which have brought in such measures they have been both popular and effective, without putting shops out of business."
Ash urged the Government to announce a complete ban on vending machines, saying moves to locate them away from areas used by children had failed.
Ms Arnott said: "Further restricting access to vending machines as opposed to banning sales of tobacco products altogether is a half-baked measure.
"It will do little or nothing to reduce under-age smoking, whilst incurring additional costs to vending machine manufacturers."
