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They soon made the breakthrough, as in the 18th minute Marten de Roon's low shot broke kindly inside the box to Denis, who calmly sent the keeper the wrong way and slotted into the corner.
Atalanta doubled their lead seven minutes later when Nicolo Cherubin rose highest in the middle to head Gomez's corner into the net.
It was almost three for the hosts on the stroke of half time as Maximiliano Moralez raced onto Gomez's pass and fired narrowly wide of the post.
However, just three minutes later De Roon crashed a low drive from the edge of the box into the bottom corner to make sure of the three points for Atalanta.