The Mac maker was expected to unveil an iPhone 5 at the start of this month but delivered an improved 4S.
That disappointment on the phone front was the vendor's undoing with it shipping 17.07m units in the fiscal fourth quarter, well down on the expected 20m.
Revenue of $28.27bn was also down on expectations by about a billion and net profit of $6.62bn meant that earnings per share fell below expectations as well.
The last time Apple missed earnings expectations was back in 2001 and last night its shares took a tumble dropping by 7%.
Apple sold 11.12m iPads in the three months ended 24 September and continues to increase its sale of Macs with 4.89m going out the door but on the iPod front there was a year-on-year sales decline of 27%.
Cook said that it was confident that the iPhone 4S would deliver in the next quarter, it has already broken sale records for the vendor after its launch this week shifting 4m units in just the first three days.
"Customer response to iPhone 4S has been fantastic, we have strong momentum going into the holiday season, and we remain really enthusiastic about our product pipeline," he said.