Up against Inter's midfield trio of Esteban Cambiasso, Hernanes and Mateo Kovacic in Walter Mazzarri's preferred 3-5-2 formation, Seedorf sacrificed the flanks and sent Milan out in a 4-4-2 with a diamond in midfield.
Nigel de Jong anchored Milan's midfield with Riccardo Montolivo and Andrea Poli ahead of him, while Adel Taarabt sat in behind forward duo Mario Balotelli and Kaka.
De Jong scored the only goal for the game as Milan won their first derby since 2011 and Seedorf was thrilled with how his formation change hindered Inter.
"I have to congratulate my players who played a very good game tonight and it wasn't easy for many different reasons," the Dutch coach said.
"We changed something tactically to try to surprise Inter and be more dangerous when we were attacking but also to defend against the three Inter midfielders who are usually very dangerous."
While De Jong may have scored the winning goal in the 65th minute, heading Balotelli's free-kick home from inside the six-yard box, Seedorf was more interested in his compatriot's job on Inter forward Rodrigo Palacio.
"De Jong was playing on Palacio and I think this was the key for our victory," the 38-year-old said.
Having ended a run of five Milan derbies without victory, Seedorf revealed it was a 'very special' experience but different to winning the match as a player.
"Tonight it has been a very special night for me, very intense but very nice at the same time," Seedorf said.
"The feelings you have as a player or as a manager are different but they are both special. Tonight I was more happy for the players rather than for myself.
"It is a different joy but still a very strong joy. At the end of the game it was beautiful to see them being acclaimed by our supporters, as it happened to me so many times when I was a player."
