The Spaniard tried to head the ball back to goalkeeper Bernd Leno around the hour mark, but it was intercepted and Rafa Silva scored.
That put Benfica 2-1 up on the night and had Arsenal staring down the barrel of a last-32 Europa League exit for the second season running.
Kieran Tierney and then Pierre-Emerick Aubameyang struck, however, to send Arsenal through and Arteta admitted that was huge for Ceballos.
“I’m especially happy for Dani because he is a player who lives this profession like the most important thing in his life, and when he made that mistake if that would have cost the team and gone out of the competition that would have been mentally really tough,” he said.
“That is when you need the players in the team like the ones we have with Auba, Bukayo [Saka] creating the situations, Kieran scoring the goal to save him and out of a difficult situation we created a really nice moment.”