Adamant that he checked his swing, Pedroia first barked as he walked out of the batter's box, then continued to yell from the dugout. Nauert finally warned Pedroia, who appeared to be silent by the time the eighth inning ended.
The Red Sox didn't score in the inning, although Adrian Gonzalez followed Pedroia with a bases-empty double.
"It looked like he checked his swing from our vantage point," manager Bobby Valentine said. "Then Adrian hits one off the wall, of course. Can't get it back."
Pedroia took the field for the ninth and didn't look at Nauert. Five pitches into the inning, Red Sox lefty Craig Breslow hit David Murphy with a pitch. Standing at his position, Pedroia made a swinging motion to Nauert, who then promptly ejected Pedroia.
"I was watching," Valentine said of his concern Pedroia could be tossed. "I wasn't expecting another play, you know? There was a play, and [Pedroia] made an innocuous comment and he got thrown out. It's not like he went out on the field and was yelling at him the whole time. He stayed all the way from him, he stayed totally away from him. Then Bres throws that pitch, and he makes some comment and gets thrown out. Whatever."
Valentine was animated, too, but he was not ejected. Pedro Ciriaco replaced Pedroia at second base.
"I was pretty angry and supporting my guy and probably said more to [Nauert] than I said other times I've gotten thrown out," Valentine said. "And I don't like staying on the field that long, [with] my pitcher on the mound, too."
Three of the four umpires on Tuesday -- Nauert, Dana DeMuth and Doug Eddings -- were part of the crew that Valentine criticized following a June series against the Nationals at Fenway.
"It's not right. Good umpires had a real bad series," Valentine said following a 4-3 loss on June 10. "Real bad series. And it went one way."
Pedroia's lone other Major League ejection came on Aug. 19, 2008, in Baltimore -- also on a check-swing call. Home-plate umpire Bob Davidson made that ejection.
Pedroia did not speak to reporters after Tuesday's game.