Rays catcher Dioner Navarro protested, bringing manager Joe Maddon out of the dugout. After convening, the umpires left the filed to review the tape, a process that took 2 minutes, 15 seconds to back the onfield call.
Boston, which beat Baltimore 5-4 on Wednesday, moved within three games of Tampa Bay in the division.
Edwar Ramirez (5-1) worked out of a bases-loaded, no-out jam after Carl Pavano ran into trouble in the fifth. He was the winner despite facing only three batters as the Yankees extended their road winning streak to a season-high six straight.
Rodriguez, who has two homers and nine RBIs in the first three games of 10-game, four-city road trip, had a run-scoring double in the third off Edwin Jackson (11-9) and a RBI single in the fourth against Chad Bradford. The home run was his 31st of the season and 549th of his career, breaking a tie for 12th place with Mike Schmidt on the all-time list.
Robinson Cano, Ivan Rodriguez and Jason Giambi had RBI doubles off Jackson, who lasted 3 1-3 innings.
The Rays, who had one hit after the fifth inning, lost a series for the first time since the All-Star break.
It was the third time since the break that Tampa Bay lost consecutive games. The Rays had been 12-0-1 in series since losing a season-high seven straight games from July 7-13 to turn a five-game lead over the Red Sox into a half-game deficit.
While the Rays weren't charged with any errors Wednesday night, sloppy defense contributed to four infield singles and helped the Yankees advance baserunners at will on hits to the outfield.
In losing the series opener 7-2 on Tuesday night, the Rays ran themselves out of a potential big inning and committed a throwing error that helped New York break the game open after Xavier Nady hit a two-run homer.
The Yankees built a 6-1 lead for Pavano. The right-hander, making his third start since returning from elbow surgery that sidelined him for more than a year, couldn't get through the five innings required to get the win.
B.J. Upton singled and Carlos Pena walked to begin the fifth against Pavano, who was replaced by Ramirez with New York leading 6-3. Cliff Floyd lined a single off second baseman Cano's glove to load the bases with no outs.
The Yankees escaped unscathed when Willy Aybar lined into a double play to Cano, who stepped on second before Pena could get back to the bag. Eric Hinske popped to Derek Jeter, ending the threat.
The Rays scored on Floyd's first-inning RBI double and Gabe Gross' two-run homer in the fourth as Pavano allowed six hits, walked two and struck out one in four-plus innings - his shortest outing since coming off the DL. Akinori Iwamura added an RBI double off Jose Veras in the ninth.
Jackson, who had won six of his previous seven decisions, allowed six runs and 10 hits in his shortest start of the season.
Four of the hits were infield singles, and two of the five doubles he yielded would have been singles if Bobby Abreu and Ivan Rodriguez hadn't been aggressive in taking an extra base.
