The Italy international unleashed an incredible 40-yard strike which found the top corner in the 86th minute at the San Siro.
It was the kind of strike Seedorf knows Balotelli can produce and the coach said self-belief was the key to the 23-year-old's goal.
"It's the kind of goal Mario knows how to score, as he has these weapons in his armoury," Seedorf told Sky Sport Italia.
"The great thing is that the team continues to believe in the result, as you don't score goals like that unless you believe."
The goal came during a week in which Seedorf, whose side are 10th in the league, said Balotelli still had work to do to be considered a champion.
But the Dutchman felt his words were taken out of context and believes Balotelli will, eventually, become a champion.
"People like to take my words out of context. I didn't say Mario isn't a champion, but that he will become a champion. I believe in him a great deal and I believe in the man he is becoming," he said.
"I only think positive things towards him. What position do I like him best in? I like Balotelli, full stop. He can play on the right or the left."
Kaka is expected to be fit for Wednesday's UEFA Champions League clash against Atletico Madrid despite hurting his ankle.
Seedorf praised his team's fight against Bologna, but expects Atletico to pose an entirely different challenge.
"The team fought hard. It wasn't a great game, but it's not easy when your opponents sit and wait for 90 minutes. Atletico do not play the same way as Bologna, who defend very deep," he said.
"Michael Essien has to play against Atletico, so I decided not to risk him tonight. We are working for the future and Milan's results this season will influence the choices for next term."
