It has so far been a troubled season at the San Siro with coach Massimiliano Allegri confirming last week that this season will be his last at the helm.
But a brace from Kaka and a third from Bryan Cristante gave Milan the perfect start to 2014 with a comfortable victory.
The win was just Milan's second league victory in their last 10 and moved them up to 10th while Atalanta remain in 15th.
Robinho had the first chance of the game as he shot wide from six yards and the Brazilian then tried to set up Alessandro Matri who crossed for Cristante but the 18-year-old could not get the final touch.
Cristante was having a real impact on the game and he hit the bar 14 minutes in.
It was all Milan and Andrea Consigli was forced to save a header from Antonio Nocerino before the home side eventually took the lead after 35 minutes.
Urby Emanuelson provided the through ball and Kaka beat the offside trap to coolly slot home with the side of his foot to bring up his landmark.
During the celebrations the Brazilian was handed a Milan shirt with 100 on the back and he held it aloft to a rapturous San Siro crowd.
Cristian Raimondi saw a well-struck effort for Atalanta hit the post as the half drew to a close and they had a good chance after the interval as German Denis fired over the bar.
The visitors were beginning to apply pressure and thought they had an equaliser in the 53rd minute when Yohan Benalouane applied a low finish but play had been stopped for a foul on Philippe Mexes.
Christian Abbiati was then called on to make an impressive save from Denis and the Argentinian soon went close again as Cristian Zapata blocked his shot on the line.
And the visitors were made to play for not taking their chances as Kaka doubled Milan's lead with 25 minutes to go.
Mario Balotelli supplied a low cross which hit Robinho and fell kindly into the path of Kaka who scored his second from close range.
Just two minutes later it was 2-0 and this time it was all Cristante as the midfielder approached the Atalanta area and hit a low shot from 25 yards which went in off the post.
Balotelli and Kaka both brought further saves from Consigli as the game wound down and Milan eased to a comprehensive victory.