Massimiliano Allegri's side, who have also reached the semi-finals of the Champions League, meaning they must play Monaco next Wednesday, were hoping to secure their sixth straight Scudetto with victory in this Friday night match and then in their subsequent meeting with Torino.
They would have needed second-placed Roma to drop points in Sunday's derby game against Lazio, but triumph in the Eternal City would now bring the Giallorossi to within six points of the leaders, with four games remaining including a head-to-head clash in two weeks' time.
Andrea Conti ensured it would be a difficult evening for Juve with a deserved opener just before the break, with Leonardo Spinazzola later scoring an unfortunate own goal to level proceedings.
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Dani Alves headed what looked like a late winner as Allegri's men took control, but there was a late twist as Swiss midfielder Freuler split the points.
Juve arrived in Bergamo fully aware of just how dangerous Atalanta can be, with their home statistics making for difficult reading for the reigning champions.
If the Bianconeri were to become only the fourth visiting team to take all three points at the Stadio Atleti Azzurri d'Italia this season, they needed to start well as Atalanta regularly strike early at home.
However, their hosts for the evening were content to soak up the pressure for the first half-an-hour, even finding enough space to tease Juve with sighters.
Sami Khedira lost patience and launched a ball forward for Gonzalo Higuain, whose weak volley was easily punched clear by Etrit Berisha.
Atalanta responded excellently with Gianluigi Buffon having to make a desperate run from his goal-line to deny Freuler a free shot.
Juan Cuadrado should have done better when he connected with Giorgio Chiellini's cross at the other end and, in the 40th minute, Atalanta were back on the attack with Hans Hateboer unlucky to come up short on Spinazzola's ball into the box.
On the stroke of half-time, Conti gave Atalanta the lead. Alejandro Gomez's first attempt was wayward but it was clipped home by his team's right-back.
It was a terrible time to concede but luckily for the visitors an equaliser was delivered soon after the restart.
Miralem Pjanic's free-kick looked like it was going to miss its mark so he was grateful to Spinazzola for guiding it the rest of the way with an errant header.
Juve tried to hit their hosts while their spirits were low and Paulo Dybala's snapshot was saved before Berisha got gloves to a powerful Higuain effort.
The Albanian goalkeeper, on loan from Lazio, had to do even better in the 67th minute when forced into a wild parry by the rampaging Khedira. The Germany international was fired up and kept Berisha working hard with a bullet header on Pjanic's corner.
The screw continued to turn and Juve came closer still when Pjanic fizzed a free-kick inches past a post. It was a warning that Atalanta failed to heed.
In the 83rd minute the Bianconeri rushed forward en masse and the Nerazzurri back-line were slow to react when Pjanic swung the ball across the area to the far post, where Alves was waiting to head home before tearing off his shirt as he wheeled away in celebration.
The Brazilian flyer's joy was short-lived, however. With a minute remaining, Freuler capitalised on some goalmouth madness to deposit the ball in Buffon's net from close range.
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