Lippi described the fans' reaction after his side conceded two goals as shameful and said a national team that won the 2006 World Cup and qualified for next year's finals in South Africa with a game to spare deserved more respect.
The current Azzurri coach also took exception to chants for striker Antonio Cassano, who has been overlooked despite his strong form for Sampdoria.
"You cannot allow yourself to be so arrogant," Zoff was quoted as saying by Italian media on Thursday.
"The crowd has the right to chant for who they want. Lippi can disagree with them, but he should do so with a degree of politeness."
Lippi conceded later on Thursday that he had not been very diplomatic, although he did not repent.
"I had an outburst, perhaps it was a bit strong," Lippi told the Italian Football Federation's website.
"But knowing my lads, and the enthusiasm, passion and desire they put in when they take the field, I was unable to stay quiet.
"I got angry and let off steam. That's my way of protecting the team."
The world champions came back to win in the latter stages of Wednesday's match thanks to an Alberto Gilardino hat-trick.
