Gianluigi Buffon who turned 40 on Sunday saved Papu Gomez’a tame spot-kick, after mist forced officials to watch handball incident on VAR.
While the referee completely missed a penalty shout for handball. But both incidents were difficult to make out due to the intense fog.
Juventus, who have won the Coppa Italia in each of the past three seasons, raced out the blocks.
Argentinian striker Higuain appeared to ghost past three defenders before slotting into the bottom corner to give his side a three-minute lead.
And moments later, Papu Gomez tried to take advantage of the weather, with a long range lob over the returning Gianluigi Buffon. But he got his angles all wrong.
However, the Atalanta striker was eventually given an opportunity to score from 12 yards when the referee awarded a penalty, having consulted VAR.
Marten De Roon’s backheel struck Medhi Benatia on the hand.
The referee allowed play to go on before watching a replay following the first stoppage in play and pointing to the spot.
But Buffon, who turned 40 on Sunday, celebrated his birthday in style as he parried Gomez’s tame spot-kick.
The home had more about them in the second period, but failed to create any real opportunities.
Despite being on the back foot for most of the half, Juventus still created most of the chances with Higuain going close late on.
Buffon, in his bright orange kit, looked as secure as ever in his first match after entering his fourth decade and still had time to produce a stunning late save.
With full-time looming, Buffon showed cat-like reflexes to come out and block the shot when Hans Hateboer had been played through.
Atalanta were last season’s surprise package in Serie A and the only Italian team Juventus faced and failed to beat in the calendar year 2017.
But, despite enjoying the better of the second half, they failed to find the equaliser.
All hope is not lost, though, as Atalanta stunned Napoli away from home in the last round and that will give them hope for the return leg in Turin.