Seedorf scored from the first attack of the game, firing in a 25-yard shot which went just under the bar to beat Cesena goalkeeper Nicola Ravaglia.
Cesena responded immediately. Adrian Mutu's weak header was easily saved by Christian Abbiati in the Milan goal before Gianluca Comotto's back-heel shaved the post with Mutu having another shot on goal.
The visitors kept threatening, Antonio Candreva's low cross just evading Jorge Martinez.
However, Milan almost doubled their lead midway through the first half when Urby Emanuelson's shot was deflected off Steve von Bergen before going out.
Mario Yepes and Antonio Cassano both tried their luck before the latter missed a chance to make it 2-0 when he failed to get a touch on a low cross from Ignazio Abate.
The game continued to be as open in the second half.
Ravaglia denied Stephan El Shaarawy from close range while Milan counterpart Abbiati blocked Marco Parolo's fierce shot.
Milan spurned another chance, Seedorf firing over the bar and soon after Ravaglia producing a good save from Cassano's shot from the right.
The Cesena keeper continued to thwart the hosts saving from Urby Emanuelson and Cassano but Milan just edged their visitors for their first win of the campaign.