The Italian champions had already booked their place for the last 16 with two games to spare but made sure of top spot with an impressive win.
Diego Simeone's Atletico meanwhile will have to wait until their final group game against Lokomotiv Moscow in Madrid to advance to the knockout rounds.
Juventus have 13 points from five games, with Atletico still on seven, one point ahead of third-placed Bayer Leverkusen after their 2-0 win over Lokomotiv.
Cristiano Ronaldo returned to action after recent knee problems, partnered by Dybala as in-form Gonzalo Higuain started on the bench.
The 34-year-old Portugal international was rested for last Saturday's Serie A win over Atalanta despite scoring four goals for Portugal in the international break after being substituted in Juventus' previous two games.
He had another injury scare in the opening period as he grimaced in pain and limped after colliding with the corner flag as he tried to stop the ball going out of play, but played on.
Atletico had their chances in a balanced first half with Thomas Partey sending a long-range volley wide after 13 minutes, as Juventus goalkeeper Wojciech Szczesny got down low to smother a goal-bound Saul Niguez effort.
However it was 26-year-old Dybala who was the standout player, and he got the breakthrough just before the break when he curled in a superb strike from a tight angle to leave Atletico goalkeeper Jan Oblak stunned.
Ronaldo threatened after an hour racing towards goal only to send wide, before Federico Bernadeschi rattled the post after coming on for Welsh international Aaron Ramsey.
Dybala went off to a standing ovation when replaced by Higuain for the last quarter of an hour.
Matthijs de Ligt, who had been a doubt after dislocating his shoulder at the weekend, pulled off a brilliant sliding tackle to steal the ball from the feet of a goal-bound Angel Correa with seven minutes to go.
And Alvaro Morata missed the chance to steal a point in the final moments of the game.
Correa sent the ball across the face of goal but the former Juventus striker failed to finish off on front of an empty goal.