Gonzalo Higuain's second-half brace sunk Milan at the Stadio San Paolo, but the attention was on Balotelli post-game.
The Italy international burst into tears on the bench after being substituted in the 73rd minute of the Serie A loss.
But Seedorf said Balotelli was free to express himself and described the moment as 'beautiful'.
"We are players and there are times when we express ourselves that way. I see nothing wrong or abnormal in that. I experienced it at times too," he told Sky Sport Italia.
"He too needs to grow in general. He played very well against Cagliari, while tonight perhaps didn't make the most of the space.
"These are things we can all improve on and I'm happy he has so many areas to improve, as I can help him through that education."
Speaking to Mediaset Premium, Seedorf said: "Mario is human. These are things that happen many times in football and sport in general.
"I'd say it was actually beautiful, but I'd prefer to talk about the game."
Adel Taarabt gave Milan a surprise eighth-minute lead, only for it to be cancelled out soon after by Gokhan Inler.
Higuain struck twice – in the 56th and 82nd minutes – as Napoli maintained their three-point advantage in third.
Seedorf lamented the unavailability of Keisuke Honda and Kaka and said it had a massive impact on his team's system.
"It was a step backwards in terms of the result, but I also saw many positive things," the Dutchman said.
"Unfortunately we had prepared it a certain way, then Kaka and Keisuke Honda got ill, so I had to make changes.
"We didn't have all the players to use this system. I saw Ignazio (Abate) was struggling a little in the first half, so I moved Urby Emanuelson there as I've seen him play there a few times under (Massimiliano) Allegri.
"I wanted to make two substitutions after the break, but had to preserve one, so I opted to move the players around instead."
