With Juve being held to a surprise draw at home to lowly Lecce, the Rossoneri capitalised to the full with goals from Sulley Muntari and Robinho securing the three points.
With two games remaining in the race for the Scudetto, Milan are now on 77 points, one shy of a Juve side who remain unbeaten this season.
Milan looked bullish from the first whistle and had early sighters from Kevin-Prince Boateng and Zlatan Ibrahimovic that Andrea Consigli saved comfortably.
The breakthrough arrived on nine minutes, Boateng the creator with a lofted pass from the edge of the area for Muntari, who sprang the visitors' offside trap to slide in for a controlled finish at the back post.
German Denis had Atalanta's best chance of the opening half but his header was well saved by Christian Abbiati.
Muntari, Ibrahimovic and Antonio Nocerino spurned chances as Milan bossed the second period.
Again Atalanta were only able to break out sporadically and again Denis had their best chance with another header than Abbiati comfortably kept at bay.
Ibrahimovic drilled in a shot 10 minutes from the end that Consigli held well, while the Swede and Nocerino both fired wide in the dying moments as the hosts continued to make all the running.
The second goal that Milan's performance merited finally arrived two minutes into time added on when Consigli saved from Ibrahimovic and Robinho was on hand to net with a close-range diving.