After the market closed, Shopify formally announced in a news release that it had completed the long-awaited integration.
The platform integration connects Shopify merchants to "millions of potential Amazon customers," the company said. Plans were first announced in September 2015, but it wasn't "made generally available" until December. It allows merchants to manage their product catalog for various channels — including the Amazon store — from Shopify.
Sam Kemp, an analyst with Piper Jaffray, said the move was surprising — given how long the integration process took — but it was still too early to gauge its effect on the stock. Users will be able to use the Amazon channel for free, he said, so the integration of Amazon helps Shopify strengthen its product, which should help it attract new users.
"This isn't a direct economic vehicle for Shopify," Kemp said. "Shopify won't make money on the extra volume from Amazon." However, it could make Shopify more competitive with other e-commerce platforms, such as Magento.
Shopify shares fell about half a percent in extended trade Thursday.
Earlier in the day, Rosenblatt analyst Kirk Adams said in a note that the completion of the sales partnership would be a big boost to the company, although there could be some risk for cannibalization. He maintains a current price target of $50 for the stock and expects overall fiscal-year revenue growth of 60 percent for the company.
Adams said the "ability to integrate and partner with major players in the marketplace — like Amazon and Facebook —is one reason for the firm's high opinion on Shopify.
The company currently powers more than 350,000 business in about 150 countries via web, mobile and/or brick-and-mortar locations, Adams wrote in the note.
Amazon did not respond to CNBC's request for comment.