Braintree will continue to operate as a separate service within PayPal under the continued leadership of Braintree CEO Bill Ready, eBay said in a statement.
PayPal is eBay's payment platform that enables global commerce, processing more than 7.7 million payments every day.
"Braintree is a perfect fit with PayPal," eBay President and CEO John Donahoe said.
Braintree's management team and employees are expected to stay in place, the statement said.
Braintree, that has over 180 employees, help online and mobile businesses around the world accept credit card payments by providing a merchant account, payment gateway, recurring billing and credit card storage.
Its mobile app, Venmo, which is also part of the deal, gives people a way to pay using their mobile devices.
"Together, we expect that PayPal and Braintree also will accelerate our leadership in supporting developers who are creating innovative solutions for next generation commerce startups," Donahoe said.
The transaction is subject to customary closing conditions, including regulatory approvals, and is expected to close late in the fourth quarter of 2013.
eBay anticipates an immaterial impact to PayPal's 2013 net total payment volume due to the deal. It also expects to have a negative impact of USD 0.01 - USD 0.03 to its 2013 GAAP EPS guidance due to the deal, the statement said.
"The alignment with PayPal means Braintree can continue to push the boundaries of innovation while expanding into new markets with increased speed and confidence," the Braintree CEO said.
"Our current customers and developer community can expect the same level of support and partnership they've always enjoyed, coupled with more resources," Ready added.