The grievance was filed shortly after the suspension was announced, and Papelbon lost $284,153 of his $13 million salary.
"That's business. It's not personal between Papelbon and the Nationals, or Nationals to Papelbon," Washington general manager Mike Rizzo said Monday from the MLB winter meetings in Nashville, Tennessee.
The altercation occurred in the bottom of the eighth inning of the Nationals' series finale against the Phillies, Washington's first game since it was mathematically eliminated from playoff contention.
After getting out of the batter's box slowly on a pop fly to left field, Harper, 22, returned to the dugout and was approached by Papelbon, who had been acquired exactly two months earlier from Philadelphia and had entered the game in the top of eighth.
The two appeared to have a brief but heated exchange that resulted in Papelbon putting his hands on Harper's throat and shoving him into the back wall of the Washington dugout. Several Nationals players and coaches responded immediately and separated the two.
"The behavior exhibited by Papelbon is not acceptable," Nationals general manager Mike Rizzo said in a statement at the time. "That is not at all in line with the way our players are expected to conduct themselves, and the Nationals organization will not tolerate it in any way."
In filing his grievance, Papelbon contends no precedent exists for a player's salary being withheld during a team-imposed suspension, WEEI.com reported, citing league sources.
A date for a hearing has not been set. Unless settled or withdrawn, the grievance would be heard by arbitrator Fredric Horowitz, most likely during spring training.
Information from ESPN.com's Eddie Matz and The Associated Press was used in this report.