The deal - which includes $315 per share in cash - was unanimously approved by the Panera Board of Directors.
Shares of Panera surged $38.94, or 14.2 percent, to close Wednesday at $312.94. Panera's reported net income for 2016 was $145.5 million, the lowest reported net income by the company in the past five years.
Panera sales have increased 10 percent over the past two years, just ahead of the 8 percent growth in the number of stores.
"We strongly support Panera's vision for the future, strategic initiatives, culture of innovation, and balanced company versus franchise store mix", JAB CEO Olivier Goudet said in a statement. "I have great respect for the strong business that he, together with its management team, its franchisees and its associates, has built".
In records going back to 1971, the only North American restaurant deal bigger than the sale of Panera was the buyout of Tim Hortons in 2014 by the parent company of Burger King, run by 3G Capital, according to FactSet.
JAB gave few details about its plans for Panera, which has more than 2,000 locations and about $5 billion in annual sales.
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The owner of Krispy Kreme Doughnuts and Kenco coffee will pay $7.5bn (£6bn) to take control of U.S. bakery and sandwich chain Panera Bread.
Last year, JAB acquired Krispy Kreme Doughnuts for about $1.35 billion and the year before that paid $13.9 billion for Keurig Green Mountain.
"The themes we have bet on - digital, wellness, loyalty, omni-channel, new formats for growth - are shaping the restaurant industry today". After closing at $274 a share yesterday, the stock soared to well over $300 in pre-market trading this morning.
The transaction adds to JAB's considerable holdings in the United States food and restaurant business.
"While it remains very early and details around JAB's strategic plan are not available, we believe the Panera brand will complement the private equity firm's growing presence within the coffee/restaurant space", wrote Piper Jaffray analysts Nicole Miller Reagan and Joshua C. Long in a Wednesday note.
Luxembourg-based JAB has purchased several USA breakfast and coffee companies in recent years, including Krispy Kreme Doughnuts and Keurig Green Mountain Inc.
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