The White House has confirmed it will go ahead with the nomination of General John Allen to become commander of Nato forces in Europe.
If confirmed by the Senate, Gen Allen would succeed Navy Admiral James Stavridis in the Nato post. Gen Allen is due to leave his position as commander of US and coalition forces in Afghanistan on February 10.
Defence Secretary Leon Panetta had put Gen Allen's nomination on hold last November when he directed the Pentagon's inspector general to determine whether his email exchanges with Jill Kelley amounted to wrongdoing. The emails have not been made public but were said to include flirtatious exchanges that could be judged to be inappropriate.
Gen Allen, in a brief statement through his spokesman, said he was pleased to have been cleared.
He said he was glad the Pentagon investigation concluded "the allegations against him were unsubstantiated" and that he "did not violate the requirement of exemplary conduct or the prohibition against conduct unbecoming an officer and a gentleman".
The FBI had referred the emails to the Pentagon in the course of its investigation of the Petraeus matter, which included email exchanges between Ms Kelley and Paula Broadwell, who was Mr Petraeus's biographer and later his lover.
Gen Allen had maintained from the start of the investigation that he was innocent of any misconduct.
The Pentagon announced on Tuesday that the inspector general had exonerated him.
White House press secretary Jay Carney told reporters that he hoped the Senate would consider Gen Allen's nomination "in a timely manner".