The e-commerce giant said the precise amounts won't be known until a court finalizes the deal but that the refunds will probably range from 30 cents to $1.32 for certain Kindle books purchased between April 2010 and May 2012.
In notifications to customers over the past few days, Amazon noted that publishers Hachette, Harper Collins, and Simon & Schuster have agreed to the deal in a US government lawsuit alleging a price-fixing conspiracy with Apple.
The settlements create a $69 million fund for refunds.
"We think these settlements are a big win for customers and look forward to lowering prices on more Kindle books in the future," Amazon said in a message to its customers.
The three publishers reached a settlement in April when the US government launched its case against Apple and other publishing houses "for conspiring to end e-book retailers' freedom to compete on price."
The lawsuit will proceed against Apple along with publishers Macmillan and Penguin Group for what US authorities called a conspiracy to raise prices and limit competition for e-books.
US officials said the scheme was aimed at ending a discounting effort by Amazon, which sold most e-books at $9.99 until the new pricing plan was forced on the retail giant.
The move almost instantly raised the prices consumers paid for e-books, authorities said.