The 39-year-old argued with his counterpart Stale Solbakken on the touchline after the whistle and slammed the Norwegian in his post-match news conference and television interviews.
"Ask him (Solbakken) what happened, he knows how to manipulate the media very well," Guardiola told Spanish television when quizzed about the touchline incident. "I think he has behaved very badly in this situation."
The dispute goes back to Barca's 2-0 win over the Danish champions in the Catalan capital last month, when goalkeeper Jose Manuel Pinto tricked Copenhagen player Cesar Santin into believing he was offside.
Copenhagen made a formal complaint to European football's governing body UEFA over the incident and Pinto was banned for two matches.
Guardiola took exception to comments from Solbakken on Monday suggesting Pinto's punishment was not harsh enough.
"What he cannot do is ask for a four-match ban for Pinto and say that Pinto is a bad apple," Guardiola said.
"Pinto is a player who goes in for fair play and he's an important part of our dressing room," the former Barca player added. "I don't think a coach should do something like that."
Solbakken, speaking to Spanish TV, said the club had reported the Pinto incident to UEFA to try to protect Santin and put the dispute with Guardiola down to a misunderstanding.
"I don't care if Pinto is sitting on the bench or on the sofa at home," the 42-year-old said.
"We wanted to protect Cesar because he looked stupid and had a bad time after that."
"After we had shaken hands he started to say something about UEFA and I think he meant the whistling incident," he told a news conference.
"I said that he (Pinto) should have got five games, that was just a bad Norwegian joke.
"Maybe he doesn't understand Norwegian humour, I'll have to take that on me.
"I really respect Guardiola, he's one of the finest coaches but I think he was told something wrong."
Tuesday's result meant Barca missed a chance to qualify for the last 16 with two matches to spare.
They top the group on eight points and Copenhagen are second on seven. Rubin Kazan and Panathinaikos, who drew 0-0 in Russia earlier on Tuesday, have three and two respectively.
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