Napoli appeared set to overtake Inter Milan when Uruguay forward Edinson Cavani put them 2-1 ahead in the 70th minute with his 12th goal of the league season.
Instead, Panagiotis Kone levelled with one of the goals of the season in the 86th minute, meeting a cross with an acrobatic volley from just inside the penalty area.
Napoli's stunned coach Walter Mazzarri was still absorbing that blow when Daniele Portanova got infront of the defence to head another in the 89th minute and give Bologna a 3-2 away win which kept their opponents third with 33 points.
Manolo Gabbiandini had given Bologna a 10th minute lead and Alessandro Gamberini levelled from close range five minutes after half-time.
Atalanta, who have beaten Napoli and Inter Milan this season, trailed by three goals and were reduced to 10 men after barely more than half-an-hour at the Juventus Stadium.
Andrea Pirlo's goal from a curling, dipping free-kick was the highlight of Juve's win as the title-holders went seven points clear of second-placed Inter Milan, who lost at Lazio in fourth on Saturday.
Mirko Vucinic set Juve on their way in the second minute and Claudio Marchisio scored the third as defending champions Juventus moved on to 41 points after their 13th win in 17 league games.
AC Milan were given a helping hand on their way to a 4-1 win over lowly Pescara, who gave away two own goals, while Luca Toni scored twice as Fiorentina in fifth produced another impressive performance to beat bottom club Siena by the same score.
Roberto Donadoni's Parma also won 4-1, at home to Cagliari, while Sergio Pellissier's 87th-minute goal gave Chievo a 1-0 win over sixth-placed AS Roma in fog-bound Verona.
BUFFON SAVE
"There's still a long way to go, we want to keep playing a key part in the championship, Coppa Italia and Champions League," said Juventus coach Antonio Conte. "The only way to do so is to keep working hard."
Juve's Montenegro forward Vucinic side-footed the ball past Andrea Consigli after less than two minutes, and the match could have taken a different course if German Denis had levelled shortly afterwards.
Instead, Gianluigi Buffon saved the Argentine's effort and Pirlo extended Juve's lead in the 14th minute with a 25-metre free-kick, the bearded playmaker's fourth goal of the season.
It was a no-contest after that with Marchisio adding the third from a long-range effort in the 27th minute.
Atalanta's misery was complete when Thomas Manfredini collected two yellow cards in as many minutes and was sent off just after the half hour.
Juventus eased off after that although Sebastian Giovinco and Fabio Quagliarella both had goals disallowed in the second half.
Milan, who notched up their fourth win in a row and are seventh with 27 points, needed only 35 seconds to take the lead against 18th-placed Pescara as Antonio Nocerino tapped in at the far post from Stephan El Shaar
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