Cyril Thereau gave the hosts the lead before a second-half comeback from Fabio Quagliarella and an accidental strike from Alessandro Bernardini
Cyril Thereau put the hosts ahead in the 28th minute before the champions hit back in the second half through Fabio Quagliarella and an Alessandro Bernardini own goal to seal all three points and maintain their unbeaten record this season.
Giuseppe Sannino made four changes to the Chievo side that beat Udinese 2-1 at the weekend with Claiton, Simone Bentivoglio, Gennaro Sardo and Thereau all recalled to the starting XI.
Juve boss Antonio Conte also made signifcant alterations to his team, with five switches from Sunday's 2-1 win over Chievo’s neighbours Hellas Verona, where they also fought back from a goal down.
Gianluigi Buffon and Giorgio Chiellini returned in goal and defence, with Marco Storari, Leonardo Bonucci and Carlos Tevez among those to drop to the bench.
After a cagey opening to the game, Juve began to look more threatening with Fernando Llorente, Quagliarella and Paul Pogba all firing over in the space of five minutes.
But, despite those chances for the Turin-based outfit, it was the hosts who took the lead just before the half-hour mark.
Buffon's poor clearance was brought down by Sardo, and his early pass was swept home first time by Thereau from just inside the area.
The visitors responded to falling behind brightly, with Andrea Pirlo's shot from the edge of the box deflected just over the crossbar.
Quagliarella then stung the palms of Christian Puggioni, the Chievo goalkeeper beating away an effort from distance in the 38th minute.
And Llorente wasted a golden chance to equalise two minutes before the break when Mauricio Isla's shot was deflected into his path, but the Spain international's weak header was easily gathered by Puggioni.
A minute after the interval, however, Juve were level thanks to Quagliarella. It was a scrappy equaliser, with the Italy international seeing his initial header saved, before hitting both bar and post with the rebound and finally stabbing the ball in from right on the goalline.
Two minutes later, the Sannino side thought they had retaken the lead when Alberto Paloschi converted the follow up after Buffon's fumble, but the referee's assistant had raised his flag, although replays showed Paloschi to be well onside.
As the game opened up with the hour mark approaching, Claudio Marchisio and Chiellini were both denied by Puggioni from range, with Llorente sending another weak header straight into the keeper's arms.
Juve continued to press though and went ahead in the 65th minute, as Bernardini deflected home Pogba's wicked cross from the right-hand side with Llorente waiting to pounce.
The remainder of the game saw no clear-cut chances as Conte's men closed out the match to move up to third in Serie A.