Atalanta travelled to Turin looking to cause an upset as they enjoy their best season in years under Gianpiero Gasperini.
Atalanta travelled to Turin looking to cause an upset as they enjoy their best season in years under Gianpiero Gasperini, who has steered the Bergamo side to within 10 points of Juve's lead in Serie A at the halfway point.
But Juventus were clinical in an impressive first-half that saw Paulo Dybala beat Etrit Berisha with a superb first-time strike in the 22nd minute from 25 yards then send Mario Mandzukic on his way to double Juve's lead 12 minutes later.
With one eye on Sunday's trip to Fiorentina, and with Croatian starlet Mark Pjaca fully recovered from a recent injury, Juve coach Massimiliano Allegri rested striker Gonzalo Higuain for the entire game.
Pjaca, sidelined for the past two months, replaced Dybala on the hour but it was a nervous last half hour for the hosts.
Abdoulay Konko pulled one back for Juventus on 72 minutes with a superb snap shot that beat stand-in Juve 'keeper Norberto Neto at the far top corner of the net.
Although Pjanic fired his spot-kick past Berisha and into the roof of the net three minutes later following a foul on Stephan Lichsteiner, it was far from over.
Emmanuel Latte Lath, an 18-year-old from Ivory Coast, got past Lichtsteiner to reach a low cross that sneaked past Rafael in the 81st minute.
Atalanta should have pushed the match to extra-time but Andrea Petagna's curler was finally contained by Neto.
Remo Freuler pounced on an error by Hernanes but fired over and defender Rafael Toloi fired wide in the final minutes.
Earlier, Federico Bernardeschi netted an injury-time penalty to fire Fiorentina into the quarter-finals with a 1-0 win over Chievo.
Chievo looked to have held on for extra time at the Artemio Franchi stadium until the referee pointed to the spot after Bernardeschi was felled from behind by the away side's Massimo Gobbi.
Gobbi earned a caution and Bernardeschi stepped up to send Stefano Sorrentino the wrong way with a crisp low strike into the bottom corner to seal the win.
Napoli on Tuesday sealed their place in the last eight with a 3-1 win over second division La Spezia.
AC Milan, beaten Cup finalists last year but who beat Juventus in Doha to win the Italian Super Cup three weeks ago, host Torino on Thursday.
Inter Milan, Sassuolo, Lazio and Roma all play their last 16 ties next week against, respectively, Bologna, Cesena, Genoa and Sampdoria.