The online retail and cloud computing firm says its plans will create 50,000 jobs and allow it to attract “world class talent”.
It already has a base in Seattle, Washington, and had been seeking incentives such as tax cuts and grants from a shortlist of 20 potential sites for a second home.
The company confirmed on Tuesday it had selected the Long Island City neighbourhood of Queens and National Landing in Arlington, close to Washington DC, with each getting 25,000 jobs as part of a $5bn total investment.
In addition to the headquarters, it said a new centre of operations for the US east coast would be built in Nashville, Tennessee, with an extra 5,000 people to be hired.
Recruiting will begin in the New Year, Amazon said.
The company had more than 230 bids from US cities before whittling the number down to 20 early this year.
It confirmed performance-based incentives of $1.5bn from the state of New York and $573m if it meets targets of the 25,000 people hired for the Arlington site netting an average wage of over $150,000.
Amazon said the decision to split the new headquarters followed concerns about being able to recruit and house so many people in one place.
Founder and chief executive Jeff Bezos said of the new headquarters: “These two locations will allow us to attract world-class talent that will help us to continue inventing for customers for years to come.”
Neil Saunders, managing director of research specialist GlobalData Retail, said: “In our view, the split reflects two things.
“First of all, the sheer size and scale of Amazon and its interest across many areas of technology, retail, and various consumer services. This arguably warrants multiple HQ locations as opposed to a couple of large offices.
“Second, Amazon’s forecasted strong growth means it wants to avoid the issues it had in Seattle where its expansion caused problems with the supply of labour, property, and put pressure on general infrastructure.”
He added: “While other locations may be disappointed not to have secured Amazon’s favour, it does not mean they will miss out entirely.
“Amazon is making enormous investments in warehousing, regional hubs and in retail stores. The company will expand both its customer-facing and back-end operations across America, and the world, in the years to come.”