Francisco Conceicao found Khephren Thuram with a ball inside eight seconds that the midfielder guided wide, and it wasn’t much longer before Berat Djimsiti had to block a Manuel Locatelli attempt with the visitors getting off to a blistering start.
The hosts soon settled into the game, although Charles De Ketelaere and Davide Zappacosta were both denied by a pair of Lloyd Kelly interventions.
Conceicao continued to ask questions, with Jonathan David heading wide from his cross. The winger then got behind Honest Ahanor to reach Weston McKennie’s long throw but was denied by Marco Carnesecchi, before cutting in and hitting the crossbar.
Juventus went behind in the 27th minute, though, as Gleison Bremer was adjudged to have handled Ederson’s cross after a VAR check, allowing Gianluca Scamacca to send Mattia Perin the wrong way from the ensuing penalty.
Bremer headed agonisingly past the post moments later, Ahanor denied McKennie, and Locatelli’s free-kick bounced wide as La Dea made it to the break with their lead intact.
Juventus came close to creating issues for Atalanta as they looked to restore parity, but Djimsiti did brilliantly to clear Pierre Kalulu’s pass in the box, and Ederson blocked a Federico Gatti attempt.
Debutant Jeremie Boga was introduced shortly after the hour mark for his first appearance in any competition since November and showed plenty of intent, but McKennie fired wide on the turn, and Kelly headed wide from the new man’s cross as an equaliser continued to evade Luciano Spalletti’s side.
They were then hit by two Raffaele Palladino’s substitutes at the other end, as Kamaldeen Sulemana turned home Raoul Bellanova’s cross just seven minutes after the pair had been introduced.
Mario Pasalic took even less time to score after being brought on, as he collected fellow substitute Nikola Krstovic’s pass and picked out the bottom corner to ensure Atalanta recorded just the second win from their last six matches across all competitions, setting up a semi-final against the winner of Bologna and Lazio’s match on Wednesday.
By also inflicting the first defeat from Juventus’ last five competitive matches, they condemned La Vecchia Signora to a quarter-final exit in back-to-back seasons.
Flashscore Man of the Match: Berat Djimsiti (Atalanta)