Jemele Hill and Michael Smith break down why the Red Sox are in hot water after the Yankees caught them stealing signs using an Apple watch. (1:52)

MLB commissioner Rob Manfred confirmed Tuesday that the Boston Red Sox used electronic communication from the dugout to steal opponents' signs and relay them to Boston players during games.

The New York Yankees informally reached out to the commissioner's office on Aug. 19 and filed a formal complaint against the Red Sox on Aug. 23, sources told ESPN's Buster Olney. Baseball's investigation of the Red Sox is ongoing, Manfred said from Fenway Park ahead of Boston's game against Toronto, but he expects it will be completed before the end of the regular season.

News of the investigation was first reported by the New York Times.

Major League Baseball does not have a policy against sign stealing, per se, Manfred said. The issue is the use of an electronic device in the dugout, which is against league rules.

"We actually do not have a rule against sign-stealing," Manfred said. "It has been a part of the game for a very, very long time. To the extent that there was a violation of the rule here, it was a violation by one or the other [team] that involved the use of electronic equipment. It's the electronic equipment that creates the violation. I think the rule against electronic equipment has a number of policy reasons behind it, but one of them is we don't want to escalate attempts to figure out what a pitcher is going to throw by introducing electronics into that mix.

"To the extent there was a violation on either side, we are 100 percent comfortable that it's not an ongoing issue, that if it happened, it is no longer. I think that's important from an integrity perspective going forward."

The league investigation is being conducted by Bryan Seeley, a former assistant U.S. attorney for the U.S. Attorney's Office in Washington who now heads MLB's department of investigations.

After MLB corroborated the claims with its own video, the commissioner's office confronted the Red Sox, who admitted that video replay personnel were getting signs and that those were relayed to some players, The Times reported. The scheme had been ongoing for some weeks.

The Red Sox were accused of stealing signs electronically against the Yankees at Fenway Park. Adam Glanzman/Getty Images

The Red Sox's scheme came to MLB's attention when New York Yankees general manager Brian Cashman filed a complaint with Manfred's office last month. He supplied video of what the team contended was a Red Sox trainer looking at his Apple Watch, the Times reported, and then relaying information to players -- in one instance outfielder Brock Holt and in another infielder Dustin Pedroia -- during a series between the teams in Boston.

Red Sox manager John Farrell, whose team is hosting Toronto, said that Boston is "aware of the rule [that] electronic devices are not to be used in the dugout." When asked to comment further, he said it's "a league matter."

Regarding the potential for penalties, sources told Olney it is highly unlikely the Red Sox would be docked draft picks, but that fines and suspensions are possible.

Manfred said that, "under the major league constitution," the league has the authority to strip one or both teams of wins, but he acknowledged it has never happened in a case like this, because "it's just very hard to know what the actual impact in any particular game was of an alleged violation like this."

Asked whether a potential punishment for Boston could be used to deter future incidents, Manfred acknowledged it was a factor that would be weighed.

"When I think about punishment, I think you need to think about deterrents," he said. "I think you need to think about how the violation has affected the play on the field, and I think you need to think about how it's affected the perception of the game publicly. All of those things are something that you have to weigh in terms of trying to get to appropriate discipline."

Red Sox president of baseball operations Dave Dombrowski declined to comment on the matter of electronic devices, but he said stealing signs has been part of the game for many years.

"I don't really want to comment on any analysis of anybody. But I will say I think sign stealing has been going on in baseball for a long time," Dombrowski said. "I've been in the game for 40 years, I've known of it for 40 years, sign stealing, itself. People I've talked to that played back in the '50s talk to me about sign stealing. So I do think sign stealing has been taking place for a long time. I will acknowledge that.

"Do I think sign stealing is wrong? No, I don't. I guess it depends how you do it. But no, I never thought it was wrong. I guess everybody in the game has been involved with it throughout the years. People are trying to win however they can. It's an edge they are trying to gain. Sometimes your sophistication of signs can make a difference. So no, I never felt like it's wrong. Put it this way, I was never brought up that it was wrong."

Yankees outfielder Brett Gardner, who is in Baltimore for a game against the Orioles, said of the sign stealing, "It was something we expected was going on."

During Yankees-Red Sox games this year, Yankees catchers increasingly and repeatedly visited the mound to go through the signs or change sequences verbally -- and this was related partly to the Yankees' concerns about how the Red Sox were relaying information, sources told Olney.

Sources with knowledge of the situation told ESPN's Andrew Marchand that the Yankees have suspected the Red Sox were using illegal methods to steal signs for a while, but they could not prove it until the last series in Boston. The Yankees thought something was not right because the Red Sox repeatedly hit pitches hard that the Yankees felt would normally be unhittable -- especially with runners in scoring position.

A source also questioned how Farrell and Dombrowski did not know about the scheme, considering the Yankees were able to figure it out, and so many players were involved.

The Red Sox have since filed their own complaint, alleging that the Yankees use a camera from their YES Network exclusively for stealing signs.

Sources denied the substance of the Red Sox's counterclaim, with one saying it was a public relations move to try to muddy the waters.

"There is no meat on the bone," the source said.

"No chance," Yankees manager Joe Girardi said.