The 59-year-old four-star general engaged in no "inappropriate communication" with Jill Kelley, 37, the officials said.
Kelley's May 2012 complaints to the FBI about anonymous emails led federal agents to uncover an extramarital affair between CIA Director David Petraeus and his biographer, Paula Broadwell.
Petraeus, a retired four-star general, resigned from the CIA's top post Nov. 9, 2012.
Pentagon officials familiar with the investigation told The Wall Street Journal some emails between Allen and Kelley were flirtatious, but the Office of Inspector General concluded Allen engaged in no wrongdoing, officials said.
About 15 investigators from the Inspector General, an independent agency whose mission is to oversee Pentagon programs and operations for integrity and accountability, looked into whether Allen's emails -- particularly 60 to 70 of them -- violated Defense Department policy, government regulations or military law, The New York Times reported.
The emails covered 2 1/2 years starting in 2010, when Allen was deputy commander of U.S. Central Command, based at MacDill Air Force Base in Tampa. Kelley frequently hosted social events for senior officers assigned to the headquarters.
The Inspector General office, led by Principal Deputy Inspector General Lynne M. Halbrooks, wrote to Allen in Kabul, Afghanistan, to let him know the probe had cleared him, officials said.
The agency also let Defense Secretary Leon Panetta know Allen was cleared, Pentagon spokesman George Little said in a statement.
"The secretary was pleased to learn that allegations of professional misconduct were not substantiated by the investigation," Little said. "The secretary has complete confidence in the continued leadership of General Allen, who is serving with distinction in Afghanistan."
Spokesmen for Allen had no immediate comment. Allen is married to Kathy Allen and has two daughters, Bobbie and Betty.
The Inspector General's investigation prompted Panetta to put on hold Allen's nomination to be the supreme allied commander for Europe, NATO's top military post.
Allen is to relinquish command in Afghanistan early next month.
The Pentagon has not said if it wants the Senate Armed Services Committee to reschedule Allen's nomination.
He also could be nominated to another senior post -- or he could retire, the Times said.
Key Republican members of the Armed Services Committee, including Sen. John McCain of Arizona, expressed support for Allen during the Pentagon investigation.