The 23-year-old forward made his frustration at his early exit known in an explosive post-game interview, but his boss says the forward has been behaving well lately.
The Dutchman hauled the forward off with 21 minutes remaining at the Stadio Olimpico, sending Giampaolo Pazzini on in the 23-year-old's place.
Balotelli, who also had an angry exchange with teammate Adel Taarabt during the game, looked upset with his withdrawal at the time, but that turned out to be nothing nothing compared to the rant he went on in his post-game interview.
However, Seedorf says he made the right call and also suggested that the Italy international should be cut a little slack.
"We can dispute every decision, but in my opinion Pazzini and Kaka did fairly well," the Rossoneri boss told Sky Sport Italia. "Mario was one of my three changes. In that moment, I felt it right to play Pazzini, who also went close to scoring.
"When it comes to shedding light on things related to Balotelli, we're always ready, but in these last few weeks he has done great things, also from the point of view of his behavior. Today, he didn't express himself in the best way, that's understood. But his clash with Taarabt? Everything was cleared up. These are things that happen on the pitch."
Milan's 2-0 defeat in the Italian capital ended a run of five successive defeats, thus putting its hopes of snatching a Europa League place in jeopardy.
However, Seedorf, who took over in January, insists he does not know if he will be fired if the Rossoneri fail to secure European football for next season.
"I cannot speak for the club," he said. "You must direct certain questions to [Milan CEO Adriano] Galliani.
"I know my contractual position and I know that Milan always make decisions at corporate level. But I know why they called me and I'm here to give my all."