The Cote d'Ivoire international returned to the Stadio Atleti Azzurri d'Italia and played a key role in the midfield as the Rossoneri fought back from a goal deficit to stun their hosts.
Remo Freuler's opener for Gian Gasperini's side gave Atalanta an early lead in the 33rd minute but Krzysztof Piatek's double and Hakan Calhanoglu inspired Milan's comeback win to stretch their unbeaten run to seven league games.
Kessie played for the full 90 minutes on his 22nd league game for the Rossoneri this season and has taken to social media to celebrate his side's resilience.
"Very important victory against a very strong opponent," Kessie wrote on Instagram.
AC Milan are aiming for a return to the Uefa Champions League after a five-year absence and they sit fourth in the Italian top-flight log with 42 points from 24 outings.
They welcome Empoli for next Serie A match at the San Siro on Friday.