The Spanish midfielder says that commenting on the coach's "sterile" remarks would be a "waste of time", and is backing Lionel Messi to win the Ballon d'Or award
The Portuguese coach labelled Vicente del Bosque's striker-less system "sterile" and stated that it hurt Spain's potency following La Roja's 1-1 draw against Italy in their opening match in Poland and Ukraine.
And Iniesta could not resist the urge to take a swipe at Mourinho after Spain won the tournament by playing the majority of the matches with that system - including the final, in which they defeated Italy 4-0.
"Those were opportunistic comments because of the draw against Italy," Iniesta told Barca TV. "Commenting on such remarks is a waste of time.
"We won the tournament with that system and these players, and that is something we should not forget."
The 28-year-old was named the best player of Euro 2012, but when asked about the possibility of winning the Ballon d'Or award, he backed Barca team-mate Lionel Messi to clinch the prestigious accolade.
"I am very happy to be considered the best player of the Euros," Iniesta continued. "It is great because your work on the field is acknowledged.
"This is even better because we were champions. I had very good feelings prior to the tournament, but I never thought about being the best player.
"The Ballon d'Or? This is something that I do not decide. The only thing that I am worried about is to play well and make the fans happy.
"I am not competing against anyone. I would give it to Messi."