Milik scored with an expert volley following a cross from Mario Rui three minutes after he came on for Dries Mertens. The Poland center forward has scored seven of his 15 Serie A goals as a substitute.
"It's a very important goal for me, as I hadn't scored in a while," Milik said. "Of course I want to play more and score all the time — I'm a striker — but everything isn't always exactly the way you want it to be in football."
Fabian Ruiz put Napoli ahead less than 90 seconds in by redirecting a splendid cross from Lorenzo Insigne on a counterattack. Former Napoli forward Duvan Zapata equalized after the break from close range.
Atalanta remained 11th.
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