The firm made $35bn in sales - a net profit of $8.8bn - in the three months ending in June.
The failure to meet its target is believed to be due to disappointing sales of iPhones.
Apple sold 26 million iPhones during the third quarter, missing sales targets by 2-3 million.
By contrast, the electronics giant sold 35.1 million iPhones in the second quarter.
It is believed that the loss in sales may have been a result of consumers holding off on purchasing a new iPhone amid rumours of a new handset arriving in the autumn.
This led to many predicting that Apple would fall short of expectations, as rumours over the launch of a new iPhone last year also caused Apple to miss quarterly expectations for the first time in years.
Apple also made headlines recently by claiming that it is owed $2.5bn (£1.63bn) in damages from Samsung, its rival in mobile and tablet technology.
Earlier this week Apple released its new OS X Mountain Lion operating system.