The young goal machine scored his 15th goal of the league season to defeat the hosts, who were reduced to 10 men and sit just four points above the drop zone.
Stephan El Shaarawy was the hero for the visitors, as he notched the only goal of the game 29 minutes in, while Atalanta slumped to a defeat that leaves the club nervously looking at the relegation zone down below.
Needing three points to keep up its quest for a place in the Champions League for the coming campaign, Milan found it difficult to break down the hosts in the early going. Atalanta, in fact, was the first team to threaten on goal, with German Denis forcing a save from Christian Abbiati as he fired in an effort from out wide that was comfortably claimed by the keeper.
With Milan imposing itself in the middle while wasteful in its approach play, the onus once more fell on top scorer and 20-year-old El Shaarawy to lead his side's attack. The young forward did brilliantly to twist his way to the byline, and an improvised chip with the outside of the boot momentarily had Andrea Consigli scrambling before flying just wide of the post.
The Rossoneri finally took the lead just before the half-hour mark, with El Shaarawy doing the honors. M'Baye Niang opened up the Atalanta backline with a wonderful through ball, and El Shaarawy reacted instantly to square up to Consigli and rifle into the bottom corner for his 15th Serie A strike of the season.
The goal left only Edinson Cavani ahead of El Shaarawy as the season's most prolific marksman, and Milan took advantage to establish a strong control of the match as Atalanta floundered in its attempts to level.
A header from Cristian Raimondi steered straight at Christian Abbiati was the closest the home team came to equalizing in the first half, as Milan looked comfortable spraying the ball across the pitch while the opening period came to a close.
Atalanta remained resolute, but Giampaolo Pazzini came close to a spectacular strike for Milan when his scissor-kick flew wide of the goal less than 10 minutes into the half. La Dea's plight became even worse when Davide Brivio was sent off for a second bookable offense following a brutal challenge on Pazzini.
With Denis withdrawn to make way for defender Carlos Matheu, Milan once more lowered the tempo and looked supremely comfortable in the absence of forward threat from their opponents.
There remained the occasional charge on goal - Mathieu Flamini let loose with a stinging shot that was deflected just over - but the Rossoneri otherwise looked content to play out the remaining minutes and goad Atalanta into pushing forward, subsequently punishing them on the break.
The Rossoneri have now won six of their last eight Serie A outings, and a Champions League place that once looked out of their reach now becomes a real possibility for the Italian giants.