The record-breaking launch disappointed Wall Street, however; analysts predicted up to 10 million sales. Apple stock fell more than two per cent in pre-market trading on the news.
The previous model, the iPhone 4S, sold more than four million units during its first three days on sale last year.
Analysts including Gene Munster of Piper Jaffray predicted a bigger leap in first weekend sales for the new handset. He claimed last week that sales of six million units would be a “worst case scenario”.
Tim Cook, Apple’s chief executive, admitted the firm had been unable to keep up with demand for the iPhone 5, which was introduced in 22 countries on Friday.
“While we have sold out of our initial supply, stores continue to receive iPhone 5 shipments regularly and customers can continue to order online and receive an estimated delivery date,” he said.
“We appreciate everyone’s patience and are working hard to build enough iPhone 5s for everyone.”
The best selling Android handset, the Samsung Galaxy S3, sold 10 million units in less than two months earlier this year.
Alongside its latest sales figures, Apple announced that iOS6, the new version of its mobile operating system, has been installed on more than 100 million iPhones, iPads and iPods since its release on Wednesday. It represents more than a quarter of the total iOS user base, according to figures released by Apple at its WWDC developer conference in June.
The new software has been widely criticised over errors and omissions in its Apple Maps app, which has replaced Google Maps as the default mapping application. Apple has promised the quality of its data will improve as customers report bugs and update location information.