The shares are equivalent to a almost one percent stake in the company, according to a JD.com spokesman.
Google's search engine has been blocked in China since 2010 over its refusal to censor search results to comply with local laws.
JD.com is China's second-largest e-commerce company after Alibaba.
Google is stepping up its investments across Asia, where a rapidly growing middle class and a lack of infrastructure in retail, finance and other areas have made it a battleground for USA and Chinese internet giants.
Google declined to comment on the rumoured Flipkart deal. JD.com's product range and Google's market share will help both companies achieve their goals.
Under the deal announced Monday, Google bought about 27 million newly issued shares of Nasdaq-listed JD at $40.58 apiece, a pricing based on the volume-weighted average trading price over the last 10 days.
"The announcement isn't focused on China", JD.com spokesman Josh Gartner confirmed to AFP. By applying JD.com's supply chain and logistics expertise and our technology strengths, we're going to explore new ways retailers can make shopping effortless for their consumers, giving them the power to shop wherever and however they want.
The investment may give Google access to more consumer data, which can be used to boost usage of Google Shopping, said Morningstar analyst Ali Mogharabi.