PayPal, which has more than 15.4 million accounts, allows users to deposit cash into an online account using a credit card, then release funds to a seller's account via email.
The deal, which has yet to be approved by shareholders or US regulators, could be completed by the end of the year. The PayPal brand will continue to exist, and eBay would take commission on PayPal payments.
EBay may ditch its own online payment system, Billpoint. A spokeswoman for eBay UK said if the deal goes ahead, the firm would look at "what works best for its European users".
Meg Whitman, chief executive of eBay US, added: "This brings together two companies in a way that will benefit our users."