The tech giant sold 45.51 million iPhones in the three months to 24 September, beating an average estimate of 44.8 million.
The company also forecast higher-than-expected holiday season revenue of between $76bn and $78bn.
But revenue in the fourth quarter fell 9% to $46.85bn.
That meant annual revenue fell for the first time since 2001, highlighting a slowdown in the smartphone market as well as intensifying competition, particularly from Chinese rivals.
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