With Milan finishing runners-up in Serie A, veteran Inzaghi announced earlier this week he would leave the San Siro at the end of the season, along with Alessandro Nesta, Mark van Bommel and Gennaro Gattuso.
And the striker said his goodbyes to the Rossoneri fans with an 83rd-minute goal as Milan came from behind to win.
Santiago Garcia had earlier given Novara an unexpected lead, but that was cancelled out by Mathieu Flamini.
The visitors looked strong in the opening stages and home goalkeeper Marco Amelia was twice called upon to make saves from Giuseppe Gemiti.
And Garcia put Novara ahead after 20 minutes with a left-footed strike into the bottom left corner.
Gianluca Zambrotta fashioned Milan's first real chance after 27 minutes, curling a strike just past the left post.
At the other end of the pitch, Novara gave their hosts another scare after 32 minutes with a header from Andrea Caracciolo just clearing the crossbar.
Milan had looked out-of-sorts throughout the first half but Alberto Aquilani gave them some confidence moments before the interval, turning his close-range effort inches wide.
The home side improved after the break and Zlatan Ibrahimovic brought a good save out of Novara goalkeeper Alberto Fontana with his shot from the edge of the area.
And they were level after 56 minutes thanks to Flamini, who made the most of a neat pass from Antonio Cassano to fire into the bottom left corner.
Clarence Seedorf had Milan's next chance, but could only curl his 20-yard left-footed strike past the right post.
However, Inzaghi ensured a fairytale finish to his Milan career eight minutes from time, running on to a ball from Seedorf before slotting low into the centre of the net.