The 51-year-old has been heavily linked with the vacancy at San Siro after Gennaro Gattuso's departure last month.
Giampaolo joined Sampdoria in 2016 from Empoli and guided it to 11th, 10th and ninth-place finishes respectively during his three seasons at the club.
He had been contracted until June 2020, but the club confirmed on Sunday (AEST) that he has left along with his backroom staff.
Giampaolo said: "I thank the president and everyone at Sampdoria for three incredible seasons. I had a good time in Genoa, and we had a good time together.
"My thanks to all the managers, collaborators, employees and players of the club. You remain in my heart like all Sampdoria fans."
Sampdoria president Massimo Ferrero added: "We thank Marco for the three seasons with us. We grew up together, we enjoyed a lot of satisfaction and now we wish him good luck for the continuation of his career."
If Giampaolo does join Milan, he will link-up with Paolo Maldini and Zvonimir Boban, who were named as the club's new technical director and chief football officer respectively on Saturday (AEST).