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 on Tuesday.
Dybala struck two minutes into first-half injury time. His left-footed effort whipped into the net from a seemingly impossible angle leaving goalkeeper Jan Oblak with no chance.
Diego Simeone’s Atletico will need to win their final group game against Lokomotiv Moscow in Madrid to be sure of advancing to the knockout rounds.
“I think Dybala scored a goal that we can’t recommend,” said his coach Maricio Sarri.
“The first thing a coach says when he sees someone trying to shoot from that position is ‘but why the hell are you shooting from there!’
“He did something extraordinary, he deserved the applause,” said Sarri. “It was an extraordinary piece of skill.”
Cristiano Ronaldo returned to the side and played for the entire match after missing last weekend’s game against Atalanta and was substituted in their previous two games because of a slight knee problem.
“I haven’t spoken to him yet about the pain in his knee, but he looked to be in good shape,” added Sarri.
– Lacking efficiency –
Juventus have 13 points from five games, with Atletico still on seven, one point ahead of third-placed Bayer Leverkusen who beat Lokomotiv 2-0.
“We had a good match against a great rival,” said Simeone. “We had chances but we lacked a little efficiency.
“We didn’t score ourselves, which is the most important thing in football, but we were always in the match.”
Ronaldo was partnered up front by Dybala as in-form Gonzalo Higuain started on the bench.
Ronaldo had another injury scare in the first half, grimacing in pain and limping after colliding with the corner flag, but he played on.
Atletico had their chances in a balanced first half. Thomas Partey sent a long-range volley wide after 13 minutes. Juventus goalkeeper Wojciech Szczesny got down low to smother a goal-bound Saul Niguez effort.
The 26-year-old Dybala was the standout player. He made the breakthrough just before the break when he curled in a superb strike from a tight angle to leave Atletico goalkeeper Oblak completely beaten.
Dybala’s celebrations included a military-style salute to Turkish international teammate Merih Demiral.
“It was just a joke between us in the dressing room, there was no message in that,” said the Argentine.
“It was a good goal from a tight angle, there were a lot of players on front of me,” he added.
Ronaldo threatened after an hour, racing towards goal only to shoot wide. Then Federico Bernadeschi rattled the post after coming on for Welsh international Aaron Ramsey.
Dybala went off to a standing ovation and was 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.
Alvaro Morata missed the chance to poach 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.
