The ban will hit 181 apps but anyone already using a vaping program will be able to continue using it.
Some 181 apps will no longer be available on iPhones
Apple is removing all vaping apps from its online store.
It said it had taken the decision because of growing official concerns about the impact vaping can have on health.
In the US, 42 deaths and more than 2,100 cases of lung injury have been linked to a respiratory illness tied to vaping.
Apple's decision means a total of 181 apps will not be available on iPhones, reports tech news site Axios.
In a statement given to Axios, Apple said it agreed with official warnings about the negative health impacts of vaping and the potential problem presented by the appeal of e-cigarettes to the young.
It said it took "great care" to ensure that the app store was a place people could trust to get programs for their iPhone.
The vaping apps available via Apple's store let people exercise control of some features of e-cigarettes and others simply kept people up to date with news about vaping or offered themed games.
Apple said anyone who already had a vaping app on their iPhone would be able to continue using it and transfer it to any new Apple device.
The move to eliminate vaping apps began in June when Apple decided to stop accepting any new apps related to e-cigarettes.
Research by the US Centers for Disease Control and Prevention (CDC) into the causes of the respiratory disease that caused the deaths suggests one ingredient is to blame.
The CDC said it had found vitamin E acetate - a thickening agent used in many illegal vaping products - in lung samples from 29 patients hit by the disease. BBC