Upton was hit four times during the team's four-game series in Phoenix earlier this season, sparking a beanball incident between the teams that resulted in pitchers Jason Marquis and Esmerling Vasquez getting suspended.
On Tuesday, starter Jordan Zimmermann plunked him in the left elbow with a 1-2 pitch in the fourth inning. Upton slammed his bat to the ground and walked slowly to first base. He went out to right field for the bottom of the fourth but was removed after the top of the fifth with what the team said is a contusion.
"I was a little upset about it," Upton said. "My thing is, man, control your pitches. I don't know if you were trying to hit me or not, but control your pitches. Obviously, I know what their plan is, they're going to try to come inside. So be it."
Upton said that the elbow stiffened up on him and he was unable to swing a bat. Collin Cowgill took over in left field, with Gerardo Parra shifting to assume Upton's position in right.
"It's just day to day," Upton said. "We'll make sure I can swing the bat without pain and go from there. Ice, ice, ice, and try to get the swelling down and try to get some movement back in there, get moving around."
D-backs starting pitcher Ian Kennedy hit Michael Morse in the hand with a pitch in the bottom of the fourth inning, but with a runner at first at the time, Kennedy said it was not intentional.
"I was definitely not trying to hit him," Kennedy said. "Leadoff man, again, and 2-0, and then I hit him. It's not what I'm trying to do. They weren't trying to hit Justin, 1-2 the count was, and the leadoff guy had got on that inning, too. You could tell none of them were on purpose. That's baseball."
Home-plate umpire Marvin Hudson warned both benches after Morse was hit.
"Neither pitcher, in my estimation, was trying to purposefully hit them," said Nationals manager Davey Johnson. "Upton covers the outside corner well, and if you throw him a couple pitches out there, you're going to come in on him. He kind of dives into it and leans into it, and it's the same thing with a couple of my hitters. You try to pitch them in. We've gotten hit more than most.
"I thought Upton reacted rather poorly. Obviously, we don't want to put a guy on second base in a scoreless game, and obviously, they don't want to hit Morse. It's not a retaliation, he's just trying to pitch him in. I think Upton overreacted to that."