The Nationals said Papelbon has appealed, making him eligible to pitch Friday night against the Philadelphia Phillies, who traded him to Washington in July.
Manager Matt Williams plans to use Papelbon in his normal role until any penalty is served.
"We'll deal with it when that time comes, when that game comes, if it comes, and go from there," Williams said.
After Machado had hit a go-ahead two-run homer in the seventh inning of Wednesday's game, Papelbon's first pitch to Machado in the ninth inning was up and in. Then his third pitch was a fastball that caught Machado on his upper arm.
"When you throw at somebody's head on purpose, first pitch, straight out the get-go, then you throw a curveball, then you throw again at the head, that's just bulls---," Machado said Wednesday. "You know it's coward stuff. It's just coward."
Papelbon was ejected by plate umpire Mark Ripperger.
"They just said they deemed it intentional, and they didn't give me any reason," Papelbon said after Wednesday's incident. "I don't know if they have to give me any reason or not, but perception is reality.
"If Manny thinks I hit him, then that's what he thinks. I'm not going to sit here and go back and forth whether I did or whether I didn't, because it doesn't matter. If he thinks I did, that's what he thinks."
The Associated Press contributed to this report.
Papelbon suspended for throwing at Machado
Tim Kurkjian discusses Nationals closer Jonathan Papelbon's three-game suspension for hitting Orioles third baseman Manny Machado with a pitch.
Wedge: Papelbon doesn't always do it the right way
Eric Wedge reacts to the benches clearing in the Orioles-Nationals game after Jonathan Papelbon hit Manny Machado.