Blues CEO Greg Swann said on Friday morning at a media conference at Princes Park that Pratt's decision was effective immediately, with vice-president and former premiership captain Stephen Kernahan taking over as interim president.
"Richard's decision to stand aside from his position is obviously a disappointing development for Carlton, which acknowledges the outstanding contribution he has made in returning to the club he so genuinely loves to prominence in the AFL competition both on and off the field," Swann said.
"Sixteen months ago, Richard saw fit to answer the club's call to return to Carlton as president. He deemed it an honour to accept the role, which was the culmination of his lifelong commitment to Carlton as a director, sponsor and player.
"Once again, Richard has shown his loyalty to the Carlton Football Club in standing aside at this time. He sees the need to deal with these issues personally and not have them distract the focus of the club going forward.
"Stephen Kernahan now steps into the role as interim president and he will ensure the great work of the past 16 months continues."
The ACCC began proceedings against Pratt by lodging a summons in the Federal Court on Thursday, alleging that he provided false or misleading evidence in the course of an investigation.
The summons requires him to appear before the court on July 7.
In a statement, the ACCC said Pratt was one of several Visy executives investigated in 2005 under section 155 of the 1974 Trade Practices Act as part of its investigation into alleged cartel conduct in the corrugated fibreboard packaging industry.
That inquiry resulted in civil proceedings being launched against Visy, which culminated in the company being fined $36 million for colluding with Amcor.
In the criminal proceedings launched on Thursday, Pratt is alleged to have knowingly given false or misleading evidence at the 2005 inquiry.
He had not yet entered a plea in the matter, an ACCC statement said.
The summons accuses Pratt of four counts of knowingly giving false or misleading evidence.
It alleges he said he could not recall a conversation he had on May 21, 2001 about a price-fixing arrangement between Visy and rival cardboard manufacturer Amcor's corrugated box businesses.
The matter is listed to come to court for a directions hearing on July 7 before Justice Donnell Ryan.
On Friday, prominent businessman and former Carlton president John Elliott, who himself was the subject of a legal battle with the now defunct National Crime Authority (NCA) in the 1990s, threw his support behind the Visy chief.
Elliott, who was once worth $80 million but lost it all through a series of business deals -- most notably an attempt to buy Elders which cost him $20 million -- said Pratt was being targeted because of his business status.
"I just think he's one of the most generous people this community's ever seen, he's an outstanding leader of men and this thing looks very much the tall poppy syndrome and looks like a very vindictive act in my view," Elliott told ABC Radio.
"He's innocent until proven guilty. You can't stand up there and say he's guilty, and as I said I think it looks like a very, very vindictive act.
"I mean, he's paid the penalty for that misdemeanour and admitted he did the wrong thing."
Elliott said Pratt deserved to remain Carlton president because he was innocent until proven guilty, and had done much to turn the club's fortunes around.
