From 5 March, shoppers buying drinks that contain more than 150mg of caffeine per litre of product will be asked to prove they are over 16.
The rule will affect brands including Red Bull, Monster Energy and Rockstar, all of which contain around 320mg of caffeine per litre.
But it does not affect Lucozade (121mg per litre), Coca-Cola (96mg) or Diet Coke (130mg).
The amount of caffeine in coffee can vary from cup to cup, but 150mg is roughly the amount in a double shot of espresso.
Waitrose said the move built on existing labelling guidelines, which require soft drink with a caffeine level above the threshold to carry a high caffeine content warning and state it is not recommended for children.
Simon Moore, director of technical and corporate social responsibility at the supermarket, said: "As a responsible retailer we want to sell these products in line with the labelling guidance.
"These drinks carry advice stating that they are not recommended for children, so we’re choosing to proactively act on that guidance, particularly given the widespread concerns which have been raised about these drinks when consumed by under 16s."
Morrisons introduced a a similar ban in a limited number of stores on a trial basis in 2013, but ended the trial less than 18 months later - saying that some over 16s had had difficulty buying the products legitimately, because they did not routinely carry proof of age.
Campaigners including Jamie Oliver have long sought a ban on the sale of energy drinks to children. Speaking to BBC Radio 5 Live yesterday, the chef called energy drink consumption and addiction among children a "prolific problem".
He said: "Kids are saying they are addicted to them, experiencing the lows and needing another to get back up again. Even though the industry and the companies will say we do not market to kids, you will hear the opposite from kids."