Balotelli slotted to the left of Verona goalkeeper Rafael from the spot in the 82nd minute on Sunday, after Alejandro Gonzalez clumsily fouled Kaka.
Kaka was not threatening the goal, running towards the byline, but Gonzalez slid in and brought the Brazilian down, with Balotelli's calm conversion giving Seedorf three points in the first match of his managerial career.
Seedorf – who spent a decade as a player at the Serie A giants from 2002 to 2012 – was appointed this week to replace the sacked Massimiliano Allegri, and would have been frustrated as Robinho's second-half shot deflected onto the post with Rafael well beaten.
Balotelli also spurned a host of chances, but eventually made amends as Milan climbed to 11th in the table.
Seedorf 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 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 shot over.
Juan Manuel Iturbe curled a free-kick narrowly over at the other end as Milan's intensity dropped off, but 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 Verona were more composed after the interval and offered gradual 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 normally reliable Balotelli made no mistake.
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