The US firm suffered a 9% drop in revenue to $37.5 billion (£23.2bn), with profits of $7.5bn (£4.6bn) -ahead of analysts' expectations.
iPhone sales had surged 26% to 33.8 million, while the company also sold 14.1 million iPads and 4.6 million Mac computers in the three months to the end of September this year. The cheaper iPhone 5C model, launched last month, is thought to have pegged back earnings.
Chief executive Tim Cook insisted "business was stronger than ever" despite the third consecutive earnings dip.
Apple ended the last financial year with its first annual drop in revenue for 11 years.