Third-base coach Jerry Royster separated the two players. Manager Bobby Valentine and pitching coach Randy Niemann were also right next to Pedroia and Aceves during part of the argument.
Moments later, as Valentine tried to approach Aceves, the righty seemed to tell his manager to get away from him, waving his arms.
"I'm not sure it was a big flare up," Valentine said. "It was just about positioning. Dustin told him he moves when he gets the sign. He wanted to kind of move him on his own. It's Alfredo being Alfredo and Dustin being a baseball player."
By the time the game had concluded, there didn't appear to be tension in Boston's clubhouse. Aceves sat in the middle of the room and ate his postgame meal, even smiling a few times as he sat next to Jacoby Ellsbury.
Pedroia and Aceves both declined to go into details.
"That's none of [the media's] business," Pedroia said. "It's between teammates."
"You're saying that I was upset," Aceves said to a reporter. "Nobody was upset. [It's] things about our team. OK? It was something that we have to communicate on, between us, but that's us. That stays with us. That's part of the game. Whatever happens in the game stays in the game."
Perhaps it was only a matter of time before some frustration boiled over for the Red Sox, who are 0-5 on this nine-game West Coast road trip and 62-72 on the season.
"Stuff happens," said right fielder Cody Ross. "It would be worrisome if stuff didn't happen -- if we were just sitting back and letting it. When you're not playing well, guys get upset. It happens."
The incident comes eight days after Aceves stormed into Valentine's office and had a tantrum about not being used in a save situation.
The next day, Aceves received a three-game suspension.
Aceves was not permitted to fly with the team for this West Coast trip, which started Tuesday in Anaheim, the same day his suspension ended.
In his first game back, Aceves was used as the closer, but only because Andrew Bailey was unavailable due to recent work usage.
Saturday marked the third straight appearance in which Aceves worked in middle or long relief, with his team losing when he came in.
Against the A's, Aceves went three innings, giving up three hits and a run. For the season, he is 2-9 with a 4.73 ERA.