The Dutchman's second-half header secured the three points for the hosts as they narrowed the gap between them and their archrivals to just three points.
Nigel de Jong grabbed the only goal of the game as AC Milan bettered bitter rivals Inter to create a rare bright spot in a forgettable Serie A campaign.
On a day when Juventus completed a title defense in which it has barely passed a glancing look in the direction of its traditional foes, the Milan-based sides illustrated why they have not challenged for a Champions League place, let alone the Scudetto, in a contest lacking quality.
Indeed, while the fixture historically bears huge significance at the top of the table, the main factor surrounding this encounter was its impact on Milan's hopes of qualifying for the Europa League.
Although Europe's secondary competition hardly seems befitting of a club of Milan's stature, Clarence Seedorf’s men did at least bolster their hopes and are now just a point behind sixth place.
De Jong was the hero, powerfully heading home a fine free kick from Mario Balotelli, for whom the assist will have been extra sweet given it came against his former club.
Inter did at least show some added fight after going behind, but Milan held on the claim just a second win in the last seven derbies.
The tone was immediately set as Walter Samuel dived into a crunching challenge on former teammate Balotelli.
That was to prove one of the few memorable moments during the opening exchanges, however, as both sides struggled for fluency.
As if to illustrate the sloppy nature of the contest, one of the few pieces of ingenuity - a fine Adel Taarabt through ball - was completely wasted when Mattia De Sciglio hit a shot tamely into the side-netting.
That effort was in stark contrast to the one produced by Kaka when the next good opening arrived.
The Brazilian ran on to a searching long ball from De Jong, who had just dispossessed Jonathan in unsurprisingly robust fashion, before unleashing a superb half-volley that rattled against the crossbar.
It was Inter who created the first opportunity of the second period, although Mauro Icardi could only mis-hit a clever, pulled-back corner over the crossbar.
A set piece almost proved crucial at the other end, too, as Philippe Mexes headed Kaka's curling centre just wide.
Inter paid for not heeding that warning as De Jong powerfully headed Balotelli’s wonderful delivery home with 65 minutes gone.
Suddenly awakened, Inter pressed forward immediately and were almost rewarded when Hernanes just missed the target.
Balotelli saw late attempts to cap his solid performance with a goal thwarted, yet it mattered little as the hosts held on for the victory.
The Nerazzurri, by contrast, offered little in the closing stages - with Javier Zanetti in particular left to reflect on a disappointing finale, as he was denied what would have been a farewell derby appearance by failing to get the call from the bench.