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.
The Pentagon said Defence Secretary Leon Panetta was told about the conclusion of the investigation. A spokesman said: "The secretary was pleased to learn that allegations of professional misconduct were not substantiated."
He said Mr Panetta has "complete confidence" in General Allen's leadership.
The matter was referred to the Pentagon in November by the FBI during its investigation of emails between Mr Petraeus and his biographer-turned-lover, Paula Broadwell. The FBI found emails between Mr Allen and Jill Kelley, who was said to have received threatening emails from Ms Broadwell.
The White House has not decided whether to go forward with the Nato commander nomination.
General Allen had maintained he did nothing wrong in his communications.
l Mr Panetta has lifted the military's ban on women serving in combat, a move that could open thousands of front-line jobs to women.