Shares of the Scottsdale, Ariz., company rose 2.5% to end at $88 on Wednesday.
The transaction is expected to close in the first quarter of 2021 subject to regulatory approvals.
GoDaddy said it will also pay $45 million in deferred cash payments over three years subject to certain performance and employment conditions.
"Commerce is critical to our customers and we continue to invest in building seamlessly intuitive experiences that enable small businesses to sell everywhere," said CEO Aman Bhutani, in a statement on Tuesday.
"Poynt accelerates our strategy to provide a complete suite of commerce and payment services to address this critical customer need and focus on a large addressable market opportunity," Bhutani added.
Poynt is a startup run by former Google and PayPal executive Osama Bedier.
"Poynt has spent the past seven years building the most advanced connected commerce platform on the market," said Bedlier in a statement.
"Our team is super excited to join forces and help millions of GoDaddy entrepreneurs sell everywhere, in the most seamless experience possible, at a time they couldn't need it more."
After the close of the transaction, Bedlier will join GoDaddy's leadership team to head a new commerce division dedicated to small businesses and will report to Bhutani.
The Palo Alto, Calif., company generates $16 million in revenue through its network of 100,000 merchants, the company said.