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The move follows a similar decision by rival bookseller Waterstone's in 2006, and came as Borders posted losses of $73.6m (£37.5m) for the fourth quarter of last year.
The company also said that it may be selling its 71 UK stores, citing increased competition from online retailers and tough retail conditions.
Amazon has handled Borders’ online sales and customer service since 2001, paying the company a percentage of its sales. It has been estimated that the loss of Borders could cost Amazon $80m (£40.8m) to $160m (£81.6m) in annual revenue.
Borders’ new site, which has been under development since last autumn, will be used to extend in-store programmes like its rewards programme to the web.