Atalanta left it late to overcome their Tuscan visitors as they ended a three-game winless run.
Atalanta, who last month were being tipped for a place in next season's Europa League, left it late to overcome their Tuscan visitors.
Empoli fired a warning when Levan Mchedlidze got on the end of a free-kick six minutes after the restart to flick the ball past Marco Sportiello at the goalkeeper's far post.
It gave the visitors hope of claiming their first pair of consecutive league wins since December 2015, but Kessie, a towering striker who is already courting interest from a number of top clubs, was a game-changer.
After celebrating his 20th birthday on Monday, he replaced Jasmin Kurtic at half-time and on 74 minutes picked up a loose ball on the edge of the area to beat Lukasz Skorupski with a vicious low drive inside the keeper's near post.
Atalanta fought till the bitter end and after Kessie battled to keep possession wide on the left, he whipped in a cross that came off two bodies before Marco D'Alessandro poked the loose ball into the net for a last-minute winner.
Atalanta finish 2016 among some prestigious company, with only AC Milan, Lazio, Napoli, Roma and champions Juventus above them.
Empoli remain fourth from bottom, five points above the relegation places.
Juventus are due to face AC Milan for the Italian Super Cup in Doha on Friday, meaning their respective fixtures have been postponed until February.
Inter Milan host Lazio on Wednesday when a win for the visitors, fourth at eight points behind Juve, could move as high as second with a win.
City rivals Roma, who are without defender Kostas Manolas and midfield pair Radja Nainggolan and Daniele De Rossi after the trio suffered injuries in a 1-0 defeat to Juventus on Sunday, entertain Chievo with a one lead over the two teams below.
Third-placed Napoli travel to Fiorentina on Thursday on the back of a thrilling 5-3 win over Torino that saw Belgian Dries Mertens hit four goals.