Airline CEO Sir Tim Clark confirmed the order in a statement on Wednesday.
According to Bloomberg's Andrea Rothman, the two additional A380s come from Skymark Airlines' canceled six-aircraft order.
Airbus scrapped the Japanese budget carrier's $1.7 billion order in July of 2014 after the airline fell behind on its financial obligations.
Later that year, the airplane maker sued Skymark in an attempt to recoup some of the delinquent payments.
In January of 2015, Skymark told Bloomberg that it could go out of business if it had to pay Airbus a breach-of-contract penalty.
Later that month, Skymark filed for bankruptcy protection, citing weak Japanese currency, fuel contracts and its dispute with Airbus.
At the time of the cancellation, Airbus had several of the Skymark superjumbos already near completion.
The Toulouse-based airplane maker has been looking to offload the airplanes ever since.
Although the order carries a list value of $865 million, it's likely Airbus offered generous discounts to push the deal to completion. Industry sources told Reuters that Emirates likely paid no more than half price for the A380s.
According to Emirates, the two ex-Skymark jets will be delivered at the end of 2017 and will be equipped with the airline's two-class interior that seats up to 615 passengers per plane.The ex-Skymark planes push Emirates' A380 order sheet to 142 aircraft. With 75 A380s in service, the Dubai-based airline is the aircraft's biggest customer.
The Emirates order balanced out Air Austral's cancellation on Tuesday of its two A380 orders.
Skymark emerged from bankruptcy last month with the help of private equity firm Integral Corp. and fellow Japanese airline ANA.