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 Obama's national security team, including Vice President Joe Biden.
The office of the Defense Department inspector general said it reviewed an unpublished Army investigation of the case, and interviewed numerous eyewitnesses. It concluded that the evidence was insufficient to substantiate a violation of any applicable legal or ethics standard by McChrystal or any of his staff.
The Pentagon inquiry also concluded that not all of the events at issue happened as reported in the 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."
Attempts by The AP to get comment from Rolling Stone weren't immediately successful.
Obama said at the time that McChrystal had fallen short of "the standard that should be set by a commanding general." He 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."