The computer software makes common actions easier, such as letting users view two open windows at once with a split-view screen.
The total exceeds the 10 million sold in the opening weekend last year for the previous versions of Apple's smartphone.
Despite warnings from Apple, users continue to alter their iPhones to be more flexible.
Company reports that its smartphone division also had some trouble in the second quarter as unit shipments fell 3 percent year over year.
Also coming soon: Skylake, the code name for Intel's sixth-generation Core processor aimed at PCs, is slated to drop during the second half of 2015.
The smartphone giant expects second-quarter operating profit to decline 4 percent and miss analysts' expectations.
The PC maker recorded a net income of $100 million, beating analysts' expectations.
HTC says that its revenue was up 25 percent in the first quarter, but its forecasts are not encouraging.
Given Apple's guidance for the current quarter, Piper Jaffray analyst Gene Munster has boosted his prediction for iPhone sales.
Thanks to its "no device subsidy" model, AT&T says it lost fewer customers to rivals than it ever has in the first three months of the year.