Defence officials said their inquiry found the concerns about the emails sent by General John Allen to be unsubstantiated.
The general was President Barack Obama's choice as the next US commander of Nato forces in Europe.
Pentagon press spokesman George Little said defence secretary Leon Panetta was told about the conclusion of the investigation. Mr Little said: "The secretary was pleased to learn that allegations of professional misconduct were not substantiated by the investigation."
He said Mr Panetta has "complete confidence in the continued leadership" of Gen Allen.
The matter was referred to the Pentagon in November by the FBI during the course of its investigation of emails between Mr Petraeus and his biographer-turned-lover, Paula Broadwell.
The FBI found thousands of emails between Mr Allen and Jill Kelley, who was said to have received threatening emails from Ms Broadwell. At the time, officials said 20,000 to 30,000 pages of emails and other documents from Gen Allen's communications with Ms Kelley between 2010 and 2012 were in question.
Shortly after being contacted by the FBI, Mr Panetta referred the matter to the Pentagon's inspector general, while expressing confidence in Gen Allen and deciding he would remain in Kabul as commander of all allied forces in Afghanistan. At the same time, Gen Allen's nomination to be the next US commander of Nato forces in Europe was put on hold.
Officials said on Tuesday that the White House had not decided whether to go forward with the nomination. Gen Allen had maintained he did nothing wrong in his communications with Ms Kelley, who served as a social ambassador for US Central Command in Tampa, Florida.
Retired general Mr Petraeus is a former Central Command commander, while Gen Allen is a former deputy commander there.