Some customers had long suspected the company used the measure to encourage people to upgrade.
Apple admitted to slowing battery performance, but said the measure aimed to "prolong the life" of the devices.
The company has now said it will replace batteries for less and will issue software in 2018 so customers can monitor their phone's battery health.
In a statement posted on its website, the firm said it would reduce the price of an out-of-warranty battery replacement from $79 to $29 for anyone with an iPhone 6 or later.
It said it was pushing ahead with measures to "address customers' concerns, to recognise their loyalty and to regain the trust of anyone who may have doubted Apple's intentions".
The firm has had eight separate lawsuits in the US filed against it over the matter, and had also been facing additional legal action in Israel and France.