Kewell was sent to the stands during the comprehensive loss in what was his first league game in charge of the League Two side.
The former Liverpool and Leeds attacker didn't contest his charge and avoided a longer stint in the stands by accepting to pay the fine.
Kewell admitted his emotions got the better of him during the loss.
"I questioned the handball and you have to change a few other things because we are chasing the game. The eagle-eyed referee sees another handball, gives it to them and they miss it so we are still in it," Kewell said.
"Then there was a cross in the box and it was one of those 'does it hit his hand, or does it not?' The referee says no, we are complaining, they go up the other end and score a goal.
"That was disappointing and that is when I get my marching orders. I said 'well done' to the referee; I said you can see one in the far corner but not one straight in front of you."
The Magpies are anchored to the bottom of League Two after seven matches and are yet to record a victory this season.
Kewell's former club Crawley Town are nine points better off in 15th position, with three wins from seven games.
Notts County head to Stevenage this weekend as they set out to get their season back on track.
