The league leaders missed talisman Cristiano Ronaldo, who was left out following a knee injury with Paulo Dybala who fired the winner against AC Milan last time out starting.
Atalanta failed to take off inside the 16th minute when Musa Barrow had his spot kick coming off the crossbar after Sami Khedira was flagged for handling in the area.
An injury to Federico Bernardeschi 26 minutes gone ended his time on the field as Aaron Ramsey entered for the record-breaking Italian champions.
Juventus finished the half the strongest as a couple of half chances found way to their doorstep but all were fluffed with Higuain the main culprit.
No changes from the bench following the start of the second half showed on either side, with the initial conglomerate set out for a second term.
Atalanta grabbed the lead in the 56th minute when Robin Gosens found space at the back post to head home Barrow's floating delivery from the right.
The evening's first change also happened a minute later as Luis Muriel came on for the provider and individual who missed the spot kick- Barrow.
Juventus pushed for the equaliser straight away and were rewarded when Higuain turned in the area to fire into the bottom corner with the help of a deflection 15 minutes from time.
The Bianconneri regained full control ten minutes later when Higuain tapped home a cross from Juan Cuadrado following a slick one-touch passing move around the area.
Juventus wrapped the matters when Higuain send a low ball from the left to Dybala, who stepped inside the area to fire into the bottom corner in time added on.