Papelbon, a five-time All Star, gave up four runs at the top of the ninth inning in Sunday's 5-4 loss to the Miami Marlins.
Brought in to close the game for the Phillies at the top of the ninth, Papelbon conceded two runs via singles, one via a ground out and the go-ahead run courtesy of a wild pitch.
Frustration boiled over when the 33-year-old finally nabbed the third out, as he looked to grab his groin while heading towards the dugout.
Umpire Joe West spotted the indiscretion towards the Phillies fans, and consequently ejected Papelbon from the game.
Papelbon stormed back onto the field to remonstrate with West, with the umpire pushing him away after the closer made contact with him.
"While I completely understand how the fans would perceive my gesture while being booed, it was not my intent whatsoever to insult the fans of Philadelphia," Papelbon said.
"If it was perceived in that manner, I sincerely apologise."