BOSTON — Though no one would say so for the record, the Red Sox believed there to be some poetic justice in the fact that Scott Proctor was the losing pitcher in the Red Sox’ 11-6 victory over the New York Yankees.

It was Proctor who grazed first baseman Kevin Youkilis in the helmet in the ninth inning on Friday an apparent act of retaliation after teammate Robinson Cano had been struck by Sox lefty Javier Lopez in the top of the ninth.

The beaning precipitated a bench-clearing incident on the field and hard feelings in the Red Sox clubhouse. The Sox felt that Proctor’s actions deserved a suspension — he was immediately ejected by home plate umpire Brian O’Nora — but found out otherwise yesterday morning.

According to multiple industry sources, the umpires’ postgame report, filed after Friday’s game, stated that Proctor’s actions were deliberate and warranted a suspension. But yesterday morning, Bob Watson, Major League Baseball’s vice president of on-field operations, overruled the umpiring crew and told the Red Sox that Proctor wouldn’t be subject to further discipline.

Proctor stood to be suspended for a period of four games, in keeping with past penalties for similar actions.

In separate conversations, Watson spoke by phone yesterday morning with general manager Theo Epstein and manager Terry Francona to explain his ruling. The discussion with Francona was long and heated according to some who overheard parts of the conversation.

Reached yesterday at his home, Watson said: “We don’t comment on such things. All I’ll say is we deemed the ejection sufficient punishment. That’s all I’ll say.”

Watson told Red Sox officials that he overruled the umpires after talking to “all the parties involved because Youkilis was hit on a 2-and-2 pitch and because catcher Jorge Posada acted as peacemaker, speaking with both Youkilis and Francona on the field.

But according to Red Sox sources, Watson never spoke to Youkilis or anyone else in the organization before making his ruling. He did speak yesterday morning with Yankees manager Joe Torre and Proctor, during which time he informed the Yankees that no additional discipline would be forthcoming.

“I just felt like there was a lot of inconsistency,” said Francona, who has had several animated discussions with Watson in the past. “I know it’s not easy to do that job and I respect the people involved, but I thought there was a lot of inconsistency there and that’s all I want to say.”

Some members of the Red Sox organization believe that as a former general manager of the Yankees — he was the GM when the club defeated the Atlanta Braves in the 1996 World Series — Watson is biased in favor of New York. As a player, Watson, who spent most of his career with the Houston Astros, played half a season with the Sox in 1979, then spent 2½ seasons with the Yankees before finishing his career with the Atlanta Braves.

Youkilis, who was told of Watson’s decision by a reporter yesterday, was incredulous that the umpires’ report has been disregarded, but declined further comment.

“I guess what this means,” said one angry Red Sox source, “is that the next time we want to hit someone, all we have to do is do it with a 2-and-2 count, then have [catcher Jason] Varitek escort [the hit batsman] down to first base.”

It was with no small satisfaction that the Sox broke the game open against Proctor in the seventh inning yesterday.

After relieving starter Mike Mussina in the sixth after Mike Lowell and Varitek began the inning with solo homers, Proctor, booed lustily by Red Sox fans, retired three of the four hitters he faced.

But in the seventh, the Sox put the game out of reach. Proctor allowed a leadoff double to David Ortiz, then intentionally walked Manny Ramirez. Facing Youkilis again, Proctor seemed unnerved, walking him to fill the bases.

Two errors by Derek Jeter, sandwiched around another intentional walk, kept the inning going, as did a run-scoring single by Coco Crisp. Of the five runs scored against him, only two were earned.

It’s unlikely, however, that the Sox felt much sympathy for his bad fortune.

Journal sports writer Steven Krasner contributed to this report.

smcadam@projo.com