This is the first domestic loss for Seedorf in what has been a fairly successful start to 2014 for Milan's head coach.
Napoli's three goals tore apart the porous Rossoneri defense, further exposing the big elephant in the room that Seedorf has to address over the summer.
Adel Taarabt was the silver lining for an otherwise putrid night for Milan, as his debut was met with one of the most stunning goals of the season and a positive display overall.
Here are five things we learned from this pivotal Serie A match.
Mario Balotelli broke down in tears on the Milan bench after being subbed off in the second half after a lackluster display.
Balotelli's inconsistency with Milan has been quite apparent lately, as he seems to drift out of games far too easily. After being taken off the field, Balotelli was slumped in his seat and began crying, a gesture that had many wondering what exactly the reasoning was.
After the match, Clarence Seedorf clarified the issue, saying that the player has had a very strange week.
According to La Gazzetta, the strangeness Seedorf was referring to happened a few days ago, when Balotelli discovered that he was in fact the father of Pia, the daughter of his old girlfriend Raffaella Fico.
Adel Taarabt's brilliant debut for Milan was capitalized on in the early minutes, when only his fifth touch of the match resulted in a near full court sprint to score a magnificent goal.
The Moroccan has shown flashes of brilliance throughout his career in England with Queens Park Rangers, but has also been criticized for being inconsistent and lazy.
Right after the goal, Taarabt went over to give Clarence Seedorf a big hug as a token of his appreciation. It would be very surprising if he didn't get another start next weekend.
Napoli recovered from their two consecutive losses—a 3-0 loss to Atalanta in Serie A, and a 3-2 defeat at the hands of Roma in the Coppa Italia—and took their frustrations out on a hapless Milan defense that has been abysmal on the road this season.
Gonzalo Higuain showed the Partenopei faithful why Napoli made him their most expensive summer signing in history by netting a fantastic brace and connecting with his teammates brilliantly.
Aside from the Argentine hitman, the rest of the midfield was able to keep great pressure on Milan and suffocate them in their own half, picking apart the Rossoneri with a flurry of pinpoint passes.
The partnership between the two French defenders Adil Rami and Philippe Mexes didn't quite work. It seemed that nearly every attack from Napoli resulted in a very dangerous opportunity. The southern Italian side shot a total of 27 times, with nearly half of those shots ending up in-between Christian Abbiati's post.
Seedorf started the game with Ignazio Abate as a right-winger but moved him to right-back in the second half. Urby Emanuelson was shifted forward while Mattia De Sciglio switched flanks. If you're confused, just imagine the players.
Milan are back to being six points down from the fifth-place side in the table, and they desperately need to find a winning formula if they want to sneak in a European place for next season.
Now that the Rossoneri have been knocked out of the Coppa Italia, their only hopes of getting into Europe is to make a late-season surge domestically, or a more difficult approach that involves winning the Champions League.
You can always dream, right?