With familiar boos from opposing fans echoing throughout Fenway Park, A-Rod ran the count to 3-0 and then pounced on a 95 mph fastball over the middle of the plate from Junichi Tazawa.
A second or two later, the ball was in the left-field seats above the Green Monster for a solo homer.
Rodriguez jogged around the bases on the pinch-hit shot that broke an eighth-inning tie and lifted the Yankees to a 3-2 win over the Boston Red Sox on Friday night.
"I'm actually very excited, trying to stay in the moment," Rodriguez said. "It's good to do it in a good team win."
Yankees manager Joe Girardi left Rodriguez out of the starting lineup to rest, but sent him up to bat for Garrett Jones with one out in the eighth. Girardi was among the first in the dugout greeting party to give Rodriguez a high-five.
"It's a big hit for us in that situation," the manager said. "Allows us to use our bullpen the way we want to use it, gives us the lead, he gets by the 660 and we move on."
It was Rodriguez's first career homer as a pinch hitter -- he was 1 for 16 in those situations -- and it came at Fenway Park, where he made his major league debut with Seattle in 1994.
"I really like this place," Rodriguez said.
Mays saluted Rodriguez in a statement released by the San Francisco Giants.
"Congratulations to Alex Rodriguez on his 660th home run. Milestones in baseball are meant to be broken and I wish him continued success throughout his career," the Hall of Famer said.
The Yankees' reaction was a bit subdued for a teammate who was suspended all last season for his involvement in the Biogenesis performance-enhancing drug scandal. Players stayed in the dugout, applauding. But when A-Rod arrived, teammates slapped his hand and enthusiastically patted him on the back.
"I think everyone realized what he was up there for," Boston manager John Farrell said. "Unfortunately a 3-0 pitch found too much of the plate."
Asked how fans should remember No. 660, Rodriguez said: "I don't know. I know that I'm very excited. A year ago today I never thought I'd be hitting home runs and helping the Yankees win. Being in the middle of it is fun again."
The milestone homer could set up a legal showdown with the team over a $6 million payment.
Rodriguez and the Yankees have a $30 million marketing agreement that calls for payments of $6 million each for up to five accomplishments, payable within 15 days of designation by the team. The accomplishments were contemplated to be home runs 660, 714, 755, 762 and 763.
But the Yankees are thinking about letting the milestones pass without making a designation. Due to his drug suspension, the marketing possibilities for the milestones have been ruined, the Yankees appear set to argue.
Still, only three players have more homers than Rodriguez -- Barry Bonds (762), Hank Aaron (755) and Babe Ruth (714).
"Any time you're sandwiched between Willie Mays and Babe Ruth, it's pretty special," the three-time MVP said.
Rodriguez's sixth homer this season came after he struggled over his previous 10 games, going 5 for 37 with one homer and two RBIs. His 659th came on Sunday, but he was 0 for 6 in his most recent game with four strikeouts and a game-ending double play in a 3-2 loss in 13 innings to Tampa Bay on Wednesday night.
"Joe had a conversation with me early this spring and he wanted us to take 3-0 swinging a little bit more serious, be a little bit more assertive," Rodriguez said. "I literally heard his voice right before that pitch."
Tazawa (0-1) took the loss.
ON A ROLL
The Yankees won for the 11th time in 13 games and retained sole possession of first place in the AL East.
Yankees: LHP Chris Capuano and RHP Ivan Nova are expected to throw Saturday. Both are on the disabled list -- Capuano with a strained right quadriceps and Nova while recovering from right elbow surgery.
Red Sox: C Ryan Hanigan left in the seventh with a broken knuckle that Farrell said will require surgery and cause a "lengthy" absence. A pitch from Tommy Layne hit Teixeira on his right wrist and the ball ricocheted off Hanigan. Teixeira and Hanigan both flung their arms in pain simultaneously. Teixeira stayed in the game, but Hanigan was replaced by Sandy Leon.
Yankees: RHP Nathan Eovaldi (1-0, 4.15 ERA) pitches Saturday in the middle game of the series.
Red Sox: LHP Wade Miley (1-2, 8.62) tries to bounce back from his second start this season in which he failed to get out of the third inning. He gave up seven runs in 2 1/3 innings Sunday in an 18-7 loss at Baltimore.
AP Baseball Writer Janie McCauley in San Francisco contributed to this report.