The title race is very much on at the halfway stage of the season after champions Inter dropped points for the second weekend in a row following last Saturday's 1-1 home draw with Cagliari.
Striker Sergio Floccari scored a superb opener for mid-table Atalanta on 18 minutes before playmaker Cristiano Doni extended their lead with a deflected free kick and a powerful header in the first half.
Jose Mourinho used all his three substitutes by the start of the second period but his side barely mustered a shot on target before Zlatan Ibrahimovic netted a consolation in injury time.
"I can't explain it," Mourinho told Sky television before he clashed with interviewers.
"I should keep quiet and let the sports press use any adjective they want, which I must accept given my team played such an awful match."
Before the Cagliari draw, Inter had won eight league matches in a row but have rarely hit top form all season.
Bergamo-based Atalanta are always a threat at home and 22 out of their 27 points this term have come in their own stadium.
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In the late game in Rome, Cristian Ledesma put Lazio ahead midway through the first half when his free kick from near the touchline was misjudged by goalkeeper Alex Manninger and drifted into the top corner.
Manninger, who has admirably filled in for the injured Gianluigi Buffon for the past three months, was only playing because the fit-again Italy keeper went down with a fever.
Sweden defender Olof Mellberg headed in the equaliser on the half hour for second-placed Juve, who hit the post through Nicola Legrottaglie in the second half among other chances.
Genoa earlier moved up to fourth, the final Champions League qualifying spot, thanks to a 2-0 win at Lecce and fifth-placed Napoli's niggly 2-1 defeat at joint-bottom Chievo.
Last season's runners-up AS Roma, who had a terrible start to the campaign, are now just five points off a Champions League place after a wonderful overhead kick from Julio Baptista in injury time sealed a 1-0 win at lowly Torino.
AC Milan in third are six points behind Inter after a 1-0 win over Fiorentina on Saturday in what could be Kaka's last game for the club if Manchester City's huge bid is successful.
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