The probe's results released Monday also called into question the accuracy of the magazine's report last June, which quoted anonymously people around McChrystal making disparaging remarks about members of President Barack Obama's national security team, including Vice President Joe Biden.
At the time he dismissed McChrystal, Obama said the general had fallen short of "the standard that should be set by a commanding general." The Defense Department inspector general's report, however, concluded that available evidence did not support the conclusion that McChrystal had violated any applicable legal or ethics standard.
Last week the White House tapped McChrystal to head a new advisory board to support military families, an initiative led by First Lady Michelle Obama and Jill Biden, wife of the vice president. The selection of McChrystal was announced on April 12, four days after the inspector general's report was finished.
The inspector general's conclusions were first reported Monday by The New York Times, which obtained the report under a Freedom of Information Act request. The Pentagon subsequently posted the report on its website.
White House spokesman Tommy Vietor declined to comment on the report.
The inspector general's report said it reviewed an unpublished Army investigation of the case and interviewed numerous eyewitnesses. It said McChrystal declined an invitation to provide sworn testimony, saying he had already testified to Army investigators. He also declined to comment on the IG's conclusions.
The Pentagon inquiry also concluded that not all of the events at issue happened as reported in the Rolling Stone article.
"In some instances, we found no witnesses who acknowledged making or hearing the comments as reported," the Pentagon report said. "In other instances, we confirmed that the general substance of an incident at issue occurred, but not in the exact context described in the article."
Rolling Stone issued a statement saying it stands behind its story, which it called "accurate in every detail."
After the Rolling Stone article was published, McChrystal was summoned to the White House and dismissed. He was replaced by Gen. David Petraeus.
Obama at the time called the dismissal the right decision for U.S. national security and said McChrystal's conduct represented in the magazine article also "undermines the civilian control of the military that is at the core of our democratic system. And it erodes the trust that's necessary for our team to work together to achieve our objectives in Afghanistan."
Associated Press writer Lolita C. Baldor contributed to this report.