Benintendi tied a career high with six RBIs by homering in consecutive at-bats off Luis Severino (9-5) when Boston scored five times in the third and fifth innings.
It was Benintendi's third career multi-homer game. In his last eight games, he is batting .484 (15-for-31) with four homers and 11 RBIs after hitting .222 during July.
Mookie Betts added a two-run single and rookie Rafael Devers hit a two-run double as the Red Sox (66-50) won for the ninth time in 10 games and moved 4 1/2 games ahead of the Yankees in the American League East.
Gary Sanchez hit a two-run homer while Chase Headley and Jacoby Ellsbury added solo shots in the ninth as the Yankees (61-54) lost for the seventh time in 11 games. Ellsbury also drove in a run with a groundout.
Boston left-hander Drew Pomeranz (12-4) extended his career-high winning streak to six games by allowing three runs and seven hits in 6 2/3 innings.
Severino saw his four-game winning start end as he allowed career highs of 10 runs (eight earned) and eight hits in 4 1/3 innings. It was his second shortest start of the season.
The Yankees opened a 2-0 lead on Sanchez's homer down the right field line with two outs in the first but the Red Sox put together an 18-minute third inning and sent nine to the plate.
With runners on first and second, third baseman Todd Frazier misplayed Eduardo Nunez's ground ball, making the error while transferring the ball from his glove to his hand. Two pitches later, Betts lined a single to left to tie the game.
Benintendi then lined a 1-1 fastball into the center-field seats for a 5-2 lead. After the Yankees scored on Ellsbury's bases-loaded grounder in the fourth, the Red Sox sent nine to the plate in a 24-minute fifth.
Benintendi made it 8-3 when he lifted a 1-0 fastball into the right-center bleachers and Devers doubled to center field against Giovanny Gallegos to bring in two more runs.
NOTES: The Red Sox placed 2B Dustin Pedroia (left knee inflammation) on the 10-day DL while the Yankees put RHP Masahiro Tanaka (right shoulder inflammation) on the DL. Boston manager John Farrell said it's too early to determine if Pedroia will be out for the season. Yankees manager Joe Girardi said he doesn't expect Tanaka to miss much more than the 10 days. ... The Red Sox recalled LHP Robby Scott from Triple-A Pawtucket while the Yankees recalled RHP Giovanny Gallegos from Triple-A Scranton/Wilkes-Barre. ... Boston LHP David Price (left elbow inflammation) completed a long-toss session for the second straight day by making throws from 120 feet without any pain. ... LHP Jordan Montgomery, who is scheduled to oppose Boston LHP Chris Sale on Sunday, was struck by a ball on the right side of his head when he was signing autographs during batting practice.