The case was one of several seen by press freedom advocates as an effort to intimidate the media ahead of a general election scheduled for November.
Nine other staff members of the weekly Myanmar Herald were acquitted in the case, which was filed by the Information Ministry last November after publication of an interview with a political analyst who described President Thein Sein as a fool.
The paper's chief editor, Kyaw Swa Win, and the deputy chief editor, Arnt Khaung Min, were fined by a court in the capital, Naypyitaw, for violating the media law by printing articles affecting an individual's reputation.
"We have to be cautious because the harassment on media freedom has increased, but we don't feel threatened by such repression," he said, describing the pre-election climate for the media as very bleak. "We will continue to do our job."
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The London-based human rights group Amnesty International said last month that the government's efforts to restrict freedom of expression had intensified over the past year.
Myanmar started moving in 2011 from a half-century of military rule to democracy, but many of its political reforms, including media freedom, have stalled.
The Daily Eleven, taking advantage of new press freedoms after the military regime made way for a civilian elected government in 2011, has published a series of stories on alleged corruption, abuse of power and inefficiency in the judicial system.
The outspoken CEO of the Eleven Media Group, Dr Than Htut Aung, was attacked last week by assailants who used slingshots to shoot steel bolts at his car, damaging the vehicle but leaving the publishing executive unhurt. The motive of the attackers remains unclear, though the attack has contributed to a chilling atmosphere for journalists.