Eder, Lorenzo De Silvestri and Mauro Icardi maintained the Blucerchiati's excellent record against the dominant force of Italian football after Fabio Quagliarella had put Antonio Conte's side in front.
Emmanuel Giaccherini added a second late on for Juve, but they were left still waiting for their first win again the Genovese club in four years.
Juve also missed the chance to have beaten every single opponent in Serie A at least once this season.
Things looked to be going well for Juve when Andrea Pirlo sent an excellent first-time ball from the halfway line over the Samp defence into the path of Quagliarella who kept his cool to thread the ball inside the near post with Angelo Da Costa getting a hand to the ball.
The former Samp striker did not celebrate out of respect for his ex-colleagues.
Juve's lead lasted little over five minutes before a foul by Giorgio Chiellini on Icardi inside the area saw a penalty awarded.
Eder stepped up to beat Marco Storari and bring the Blucerchiati level.
De Silvestro gave Samp the lead with his second goal in as many games, leaving Storari no chance with a bullet header at the near post from a corner.
Quagliarella should have brought Juve back on terms, but his shot from six yards was straight at Da Costa in the 70th minute.
Five minutes later, a burst of pace from former Juve winger Marcelo Estigarribia saw him race away from the last Juve defender before sliding the ball across the slick surface to Icardi, who could not miss the open goal from just a yard out.
The referee then awarded Juve a penalty only to change is mind after conferring with his assistant behind the goal, much to Chiellini's annoyance.
Nicklas Bedntner was sent on by Conte, but his evening did not last long as he landed badly on his arm, leaving the field and leaving Juve with 10 men as all three substitutions had been made.
The Serie A champions still did not give up the fight, though, and Giaccherini sent a shot into the top right-hand corner of Da Costa's goal in the first minute of stoppage time.
Juve were unable to find an equaliser, though, as they slipped up once again to their bogey side for their fifth defeat of the season.