There were 14 walks, two wild pitches, one passed ball and two steals on which sore-armed Jorge Posada - who took over for an injured Jose Molina - didn't even throw in the eighth when Boston padded its lead. And Yankees starter Phil Hughes lasted a career-low two innings and allowed a career-high seven runs.
"On a night that wasn't really baseball weather," Red Sox manager Terry Francona said, "we did some good things."
Matsuzaka improved to 3-0 after lasting just long enough to get the win.
"It was a stressful performance from the outset," Matsuzaka said. "I had a hard time getting strikes with all my pitches, not just the fastball."
Boston's relievers did a good job, except for Mike Timlin, who gave up a homer to Jason Giambi for the second time in the series in the eighth. David Aardsma pitched two scoreless innings after Matsuzaka, and Javier Lopez and Manny Delcarmen followed Timlin.
"We had to piece it together," catcher Jason Varitek said. "Hopefully, it gives our bullpen a little confidence."
Johnny Damon's steal after leading off the game with a walk was the Yankees' first of the season, ending a 12-game drought. It was their longest at the start of a season since 1948 when a 16-game streak ended with a double steal by Phil Rizzuto and Tommy Henrich.
But New York never led as Boston scored three runs in the first and four in the third when Hughes left with no outs. He walked three batters.
"I don't make too much of" Hughes' control problems, manager Joe Girardi said. "Obviously, it's not where we want him to be. He'll get better. He'll get where he needs to be. I have faith. I believe in my guys."
The Yankees were forced to move Posada from designated hitter to catcher in the eighth after Jose Molina hurt his hamstring and was lifted for a pinch runner. Coco Crisp and Dustin Pedroia stole without drawing a throw. Crisp then scored on Jacoby Ellsbury's sacrifice fly to make it 8-5.
"That was huge for us," Kevin Youkilis said. "A three-run ballgame is a lot different."
Lopez retired the first batter in the ninth before Manny Delcarmen got the final two outs, but didn't get a save because the potential tying run wasn't on deck while he pitched.
Closer Jonathan Papelbon pitched 1 1-3 innings for the save in Saturday's rain-delayed 4-3 win, and the Red Sox had used four relievers Friday and three Saturday.
The banged-up Yankees fell to 6-7.
"Things aren't going very good for the whole team," said Robinson Cano, batting .170 after going 0-for-5. "I'm not worried (about myself). It's (only) 12, 13 games."
Boston took a 3-0 lead in the first when Ellsbury led off with a walk, stole second and continued to third when Molina's throw went into center field for an error. J.D. Drew then walked, took third on Manny Ramirez's RBI single and scored on Molina's passed ball. Youkilis' sacrifice fly made it 3-0.
Matsuzaka walked three in the first two innings before his wildness cost him in the third. Damon walked, stole second and scored on Bobby Abreu's double.
Boston took a 7-1 lead in the third when Drew led off with a walk and Ramirez, Youkilis and Sean Casey singled, driving in two runs and chasing Hughes.
Ross Ohlendorf retired the next two, then threw a wild pitch that brought in Youkilis and allowed an RBI single by Ellsbury.
But Matsuzaka kept struggling in the fourth when he allowed three runs. Hideki Matsui led off with a double and Giambi walked. Molina doubled in a run, Alberto Gonzalez singled in another and Damon made it 7-4 with a sacrifice fly.
Matsuzaka retired the first two batters in the fifth, then walked Matsui and gave up a single to Posada. Finally, with his 116th pitch, he retired Giambi on a deep fly. Instead of his usual fast-paced walk off the mound at the end of an inning. Matsuzaka stood for several seconds after Crisp caught the ball, then walked very slowly to the dugout.
