Mattia Caldara scored both goals for Serie A's surprise package who won despite having Frank Kessie sent off after being booked twice in the space of three minutes.
An own goal by Empoli goalkeeper Lukasz Skorupski set Juventus on their way to a 30th consecutive home league win with Alex Sandro adding the second.
The results left Juventus 10 points clear of second-placed AS Roma, who host Inter Milan on Sunday, with Napoli a further two points back in third. Atalanta climbed to fourth, only three points behind their opponents.
Caldara headed Atalanta in front following a corner after 28 minutes and the defender, who is on loan from Juventus, scored the second after 70 minutes with an acrobatic volley.
That goal came just after Kessie was dismissed having been booked for a rough tackle on Amadou Diawara and three minutes later for fouling Lorenzo Insigne.
“The Champions League seems a bit of an exaggeration. It’s for Juventus, Roma and Napoli, but not for us," said Atalanta coach Gian Piero Gasperini.
"But we can dream of Europe. A victory in a stadium like this gives us credibility and we can think big."
Empoli managed to keep Juventus at bay for 45 minutes but were undone by an unlucky twist seven minutes into the second-half.
Mario Mandzukic met Juan Cuadrado's cross with a powerful header which Skorupski touched onto the crossbar but the ball bounced down over the line and an own goal was awarded against the Pole.
Alex Sandro made sure of the points when the collected the ball with his back to goal, held off his marker and scored with a shot on the turn.
(Writing by Brian Homewood in Berne, editing by Ed Osmond)
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