Balotelli slotted to the left of goalkeeper Rafael from the spot in the 82nd minute on Sunday, after Alejandro Gonzalez brought down Kaka with a clumsy challenge.
Seedorf – who spent a decade with the Rossoneri as a player between 2002 to 2012 – was appointed this week to replace the sacked Massimiliano Allegri.
The former Netherlands international immediately made his mark with six changes, headlined by Keisuke Honda's first Serie A start, while Verona were without in-form striker Luca Toni (flu) and Jorginho following his transfer to Napoli on Saturday.
The San Siro crowd roared their approval throughout the early stages, as an energised Milan started brightly.
Rafael reacted quickly to cut out an Urby Emanuelson ball destined for Balotelli, while the former Manchester City forward dragged a shot wide when played in by Kaka in the 14th minute.
Honda's first touch then let him down following an excellent Mattia De Sciglio cross, but the interplay between Kaka and the Japanese star continued to create chances, as Balotelli fired over over the crossbar.
The visitors offered little, but Juan Manuel Iturbe did curl a free-kick narrowly over at the other end as Milan's intensity briefly dropped off.
However, the hosts kept peppering the Verona goal and Balotelli had a powerful effort saved by a diving Rafael before Domenico Maietta cleared a spilled free-kick to keep out Kaka.
Riccardo Montolivo fired wide just before the break, but the away side were more composed after the interval and offered reminders of their threat on the break, mainly through Iturbe.
Substitute Raphael Martinho had a flicked effort smartly saved by Christian Abbiati and the game opened up in the final 25 minutes as Milan looked to turn the screw, with Robinho's strike – which took a wicked deflection off Maietta – agonisingly hitting the woodwork.
Seedorf's wait for the first goal of his reign continued as Balotelli and Robinho both shot straight at Rafael, while Iturbe's long-range effort forced a quick reaction from Abbiati.
But with nine minutes to go, Gonzalez gave Milan the chance to win with his poor challenge, and the ice-cold Balotelli made no mistake.