Yankees pitcher Joba Chamberlain questions his ejection from the game in the ninth inning yesterday after throwing two fastballs over the head of Boston’s Kevin Youkilis.

AP / Frank Franklin II

NEW YORK — The Red Sox and Yankees, it seems, can’t get through a series without some bad blood surfacing.

In the ninth inning yesterday, Yankees rookie reliever Joba Chamberlain threw two consecutive fastballs over the head of Red Sox first baseman Kevin Youkilis, leading to Chamberlain’s immediate ejection by home plate umpire Angel Hernandez.

“If that young man was trying to get our attention,” said Terry Francona, “he did a very good job. I can’t read someone else’s mind — you’ll have to ask him [about his intent].”

“It is what it is,” said Youkilis after the game. “Two balls over my head at 98 mph, I don’t know. Who knows? All I know is that this is the second time [he’s had an incident with the Yankees]. Scott Proctor threw up around my head [back in April]. Coincidence? I don’t know. [Chamberlain’s] got a 0.00 ERA and control of the strike zone.”

Yankees manager Joe Torre was adamant Chamberlain wasn’t throwing at Youkilis, saying the youngster, pitching in the ninth inning against the Red Sox for the first time, was nervous.

“He was trying to throw the ball through the wall,” Torre said. “The umpires have to be schooled somehow so they have a better sense of the game,” said Torre.

“It’s sad that it happened,” said Chamberlain. “There was no maliciousness behind it. I’m out there trying to win games. I have too much respect for the game.”

Crew chief Derryl Cousins came out and spoke to the media to explain why Chamberlain was ejected.

“There’s more than a little bit of history between these clubs,” he said. “Those were two pretty nasty pitches the young man threw. Up here, you need to be a little better throwing strikes and we just had to put a lid on it before there was a problem.”

The teams, of course, meet three more times from Sept. 14-16 in Fenway.

“It will be interesting to see how that plays out,” said Youkilis.

Uniform check irks Francona

Francona was livid that Major League Baseball sent a security agent into the dugout in the bottom of the second inning Wednesday night to check on his uniform.

Francona has been given multiple warnings about wearing pullover tops instead of the standard-issue uniform top. He’s explained to MLB officials that he wears the pullovers to keep himself warm, since, even in the middle of summer, he often feels chills because of side effects of some blood-thinning medication he takes.

MLB officials have suggested that he wear the uniform top underneath the pullover, which Francona has been doing. He showed that to MLB Vice President Bob Watson an hour before Wednesday night’s game.

But in an apparent effort to make sure that he hadn’t discarded the uniform once the game started, MLB sent an RSA (resident security agent) into the dugout, who pulled Francona into the runway leading to the dugout and examined the uniform.

“That’s about as embarrassed as I’ve been for baseball in a long time,” fumed Francona. “When Derek Jeter is on second base and I’ve got someone asking to check my uniform, I was a little perturbed … I asked him, ‘Can this wait a second?’ He told me no.

“Unless this guy can put on a bunt play, he ought to stay out of the [expletive] dugout.”

When asked if the Sox had any avenue to appeal the action, Francona said: “I think all the cursing I did to the guy up in the tunnel was appeal enough.”

Ramirez, Kielty updates

Manny Ramirez is scheduled to be examined again today by Red Sox physicians. Privately, the Sox are expecting that Ramirez will be out another week.

Meanwhile, Bobby Kielty took some swings in the cage yesterday morning to test his back and reported improvement. Kielty came out of Tuesday night’s game because of back spasms, then was sent back to the team’s hotel in Manhattan on Wednesday so his back wouldn’t stiffen while sitting in the dugout.

“I took some swings and felt better,” said Kielty after the game. ``I feel better.”

Kielty added that he expects to be available tonight when the Sox host the Orioles.

Around the bases…

Mike Lowell extended his hitting streak to 11 games with his single to right in the seventh. Lowell has three hitting streaks of 10 games or more this season … Lowell’s hit was the first off Chien-Ming Wang, who no-hit the Sox for the first six innings … Ironically, Francona was asked why, with Ramirez out, he had Lowell hitting fifth instead of cleanup. “[Wang] has been tough on Mike,” said Francona. Before yesterday, Lowell was hitting only .158 (3-for-19) against Wang … Hideki Okajima was charged with three runs in the eighth as the game got away from the Sox. The three runs were the most against the lefty in an appearance this season. In fact, the three runs equaled the amount of runs that Okajima yielded in the first two months of the season … The loss dropped the Sox to 29-13 in days games and saw their three-game winning streak in day games snapped …Thanks to a pulled oblique muscle, the Sox will miss Baltimore ace lefty Erik Bedard twice in the next 10 days. Going into yesterday, Bedard led the American League in strikeouts (221) and opponents’ batting average against (.212) and is tied for fourth in ERA (3.16).

smcadam@projo.com