The maker of the juice, called Pomegreat, agreed to ditch the magazine advert after a doctor complained to the UK Advertising Standards Authority (ASA).
The incident again highlights the fine line food and drink firms must walk when attempting to capitalise on growing consumer demand for healthy and functional products.
Pomegreat, owned by RJA Foods and endorsed by cholesterol charity, Heart UK, claimed in its ad: "Pomegranate juice may help to reduce the hardening of the arteries, which can cause heart disease and strokes."
The ASA interpreted this as a medicinal claim, which is not allowed for any food or drink product in the UK.
The ruling comes on the eve of new EU health claims legislation, expected to be published in January, which is intended to help firms navigate the quagmire that is devising claims for their product labels.
Producers have been watching developments closely as functional product categories show greater potential.
Pomegreat juice has performed well on the back of growing publicity extolling the virtues of the humble pomegranate fruit. Pomegranate juice sales generally have rocketed over the last couple of years.
Several studies have linked pomegranate juice to lower risk of a range of ailments, notably heart disease, but more recently also Alzheimer's, prostate cancer and even diabetes.
Researchers believe pomegranate's benefits stem largely from its high polyphenol content - reportedly twice that of red wine and up to 10 times that found in a cup of green tea.
The success of the Pomegreat juice brand has shown that juice drink categories hold enormous potential for producers looking to market so-called 'superfruits' that would perhaps not be so popular if eaten as they are.
Pomegranates are not easy to eat on their own because one fruit may contain up to 800 seeds.