The Partenopei had the chance to win the game in injury time but Gonzalo Higuain had his penalty saved by Atalanta goalkeeper Marco Sportiello.
“We had the game under control. We made a mistake in defence but we had three chances to secure the win,” the 54 year old told Mediaset Premium.
“It’s a shame. We had the game in our hands.
“I’m sorry for not winning as we would be in third place in Serie A. I think we did everything to win and deserved the three points.”
Napoli face Roma in their next league match as they look to push for a Champions League place.