After a first half in which they barely managed to string two passes together, Napoli pushed the self-destruct button after the break as their blundering defence generously helped Atalanta score three times in 20 minutes.
"We made too many mistakes, the defeat was down to unfortunate individual mistakes and not the rotation of the team," Benitez told reporters after fielding inexperienced Colombian Duvan Zapata in attack instead of Higuain, among other changes.
"We needed some fresh legs, quality and some new strength, so that's why I made some changes from the start," Benitez explained
"I would make the same choices again because, on a tactical level, we did what we needed to on the pitch today. The result came about because of our three mistakes, not because of the change of players."
He added: "We have so many games ahead of us. We play Wednesday, Saturday, then Wednesday again and everyone has to have their chance because it's not easy for a player to give his best when he plays every three days.
"Hamsik has just come back after a two-and-a-half month gap and we have a series of games in quick succession, so we have to manage this carefully."
Napoli, the biggest Serie A spenders in the close season with Higuain alone costing 37 million euros ($49.90 million), are third in the table with 44 points but have made a habit of dropping points against opponents from the lower half of the table.
They have already drawn with Sassuolo, Cagliari, Udinese, Bologna and Chievo and have taken only two points from their last three games.
"We need to analyse these individual errors, but the defeat is not down to any problems in the construction of the squad," added Benitez, insisting once again that he saw a bright future for his team.
"It is difficult to find space against teams like Chievo, Bologna and Atalanta, but we must learn to score more goals.
"We had many new players over the summer, now we have a more solid squad and a more balanced one that will be more attacking. It's not easy to be perfect in every game over three competitions." ($1 = 0.7415 euros))