Pedroia was 1-for-3, moving into a tie with Harry Hooper for eighth place on the Red Sox's all-time hits list with 1,707.
Pomeranz (3-1) allowed five hits and walked two while striking out seven. Craig Kimbrel struck out the side to notch his MLB-leading 10th save in the ninth.
J.J. Hardy and Trey Mancini each drove in a run for the Orioles. Baltimore has dropped four of its last six games while Boston improved to 4-4 on its 10-game homestand.
After Boston's Chris Sale threw at Baltimore's Manny Machado on Tuesday, Orioles starter Kevin Gausman (1-3) was ejected by home plate umpire Sam Holbrook for plunking Boston's Xander Bogaerts in the second inning with an off-speed pitch.
Gausman, who was charged with a run on no hits and one walk after throwing only 20 pitches in one-plus innings, was relieved by Richard Bleier.
Adam Jones was also ejected in the fifth inning for arguing balls and strikes. It was his first career ejection.
Boston built a four-run lead after five innings before Baltimore sliced the deficit in half in the sixth.
Jonathan Schoop hit a ground-rule double to right-center field to put two runners in scoring position with one out. Mancini's sacrifice fly to center scored Mark Trumbo from third and Hardy followed with an RBI single to left.
The fireworks resumed in the second when Gausman's 76 mph slider caught Bogaerts' leg, and Gausman was immediately tossed by Holbrook.
Gausman was in disbelief and voiced his frustrations to Holbrook, and Orioles catcher Caleb Joseph began shouting in the umpire's face.
Orioles skipper Buck Showalter also came out to argue, but neither he nor Joseph were thrown out.
Bleier came in and walked Mitch Moreland before Rutledge hit a line-drive single to left that caught a piece of a leaping J.J. Hardy's glove at shortstop, plating Bogaerts.
Rutledge entered the game in the first as a defensive replacement for Marco Hernandez, who strained his left shoulder fielding a ball at third base.
Boston added three runs in the fourth after Bogaerts reached on a Hardy error, advanced to third on a Moreland single and scored on Young's double to center.
Moreland later scored on a fielder's choice as Rutledge hit a ball to Hardy, whose throw to the plate was off target but not ruled an error.
Pedroia's sacrifice fly to left brought Young home two at-bats later.
Jones joined Gausman in the showers after he was tossed by Holbrook, evidently for arguing about the location of the second-to-last pitch of his at-bat.
NOTES: Boston issued a statement during Wednesday's game, saying it ejected a fan from the ballpark Tuesday night for directing a racial slur at another fan. The team said that fan is no longer welcome at Fenway Park. ... MLB commissioner Rob Manfred held a conference call with Orioles and Red Sox brass on Wednesday to discuss the teams' ongoing feud. Manfred warned both sides of discipline should they continue throwing at each other. "(The call was) to just basically address the last two weeks and to say enough is enough," Boston manager John Farrell said. Baltimore manager Buck Showalter was on the call but wouldn't share specifics. ... Showalter considered removing 3B Manny Machado from Tuesday's game after he was thrown at by Red Sox starter Chris Sale. "I didn't trust them not to do it again. If (Machado) gets thrown out of the game or does something that gets (him) suspended, then they win," Showalter said. ... Orioles RHP Ubaldo Jiminez (1-1, 7.43 ERA) opposes Boston's RHP Kyle Kendrick on Thursday.