The publishers have agreed to scrap clauses in their distribution contracts that keep ebook retailers from offering discounts.
The agreement follows an 18-month investigation into the ebook industry by the federal agency.
The bureau says the previous practice of banning discounts effectively reduced competition.
The deal covers Hachette Book Group, HarperCollins, Macmillan and Simon & Schuster, which publish many of the best-selling ebooks.
The bureau says a similar move in the United States produced discounts of 20 per cent or more for consumers.
"This agreement should benefit Canadian consumers by lowering the price of ebooks in Canada," John Pecman, the federal commissioner of competition, said in a statement.
"Businesses operating in the digital economy must realize that anti-competitive activity will not be tolerated, whether it occurs in the physical world or the digital one."
Booknet Canada reported last year that ebooks made up about 15 per cent of sales.