The Swede again proved the Rossoneri's key performer as the Italian champions emerged from the winter break to record a hard-earned win in Bergamo
The talismanic Swede opened the scoring 22 minutes into the game in Bergamo after strike partner Alexandre Pato had been felled in the area, and then turned provider for Kevin-Prince Boateng, who sealed victory for the visitors late on with a fine side-footed finish from an Ibrahimovic cut-back.
Both sides played their part in what was an enterprising and enthralling opening to the game but it was Atalanta who had the better early opportunities, with Simone Padoin twice firing over when well placed.
In the first instance, the winger could have been forgiven for his inaccuracy, Padoin getting under the ball as he attempted to test Christian Abbiati with a first-time effort from the edge of the box.
However, he really should have scored when his intelligent run in behind a stagnant Milan defence was picked out by Luca Cigarini’s wonderfully weighted through-ball from a free-kick on the right-hand side. Frustratingly for the home fans, though, Padoin did not even manage to get the ball on target.
Padoin’s profligacy was punished midway through the first half with a goal very much against the run of play.
The ball broke in the direction of Pato in the Atalanta area and, as he cleverly attempted to shield it, the Brazilian forward was needlessly bundled over by Thomas Manfredini.
Ibrahimovic stepped up to take the resulting spot-kick and found the bottom right corner to register his 12th goal of the season.
Milan would have been expected to take control thereafter but, in truth, it was not until the start of the second half that they threatened to add to their lead, Pato striking the post with a near-post effort from Urby Emanuelson’s header.
The let-off sparked Atalanta back into life, though, and Cigarini tested Abbiati with a well-struck shot from distance before German Denis somehow managed to hit the post from a yard out at the back stick after a corner had been flicked on to him.
However, Milan weathered the storm and then secured the points when Ibrahimovic controlled a raking crossfield pass on his chest before taking the ball to the touch-line and cutting it back for Boateng to score.
The Italian champions remain just ahead of Juventus at the top of the table on goal difference going into next weekend's eagerly-awaited Milan derby.