The decision was made after the discovery of the "discriminatory hand gesture" in a post published on social media on Thursday, the team said in a released statement.
The trainer at DC United, who hasn't been named, had his contract ended "effective immediately" and following an internal review, the team said in a short statement on Friday by the club.
"There is no place for racism, homophobia, misogyny, or discrimination of any kind in our sport and world and DC United do not tolerate any acts of this nature," the statement added.
It remains to be seen if the trainer in question will be identified at a later date.
The gesture in question is the 'okay' emoji, which has come to be associated with the far-right and now considered a racist symbol.
The club then announced that possible MLS violations have resulted in Fountas and Robertha being placed on administrative leave.
"D.C. United promptly reported the matter to the League Office at which point MLS began to gather all available information." a statement said. "The players will be unavailable for team activities during the pendency of that review. Placement on paid administrative leave is not a disciplinary measure."
DC United are currently being managed by former Everton, Manchester United and England striker Wayne Rooney.