Alfredo Aceves (1-0) allowed one run and five hits in seven innings, struck out two and didn't walk anyone to win his first major league start.
Rodriguez's 33rd homer in the sixth off Ervin Santana (15-6) extended the Yankees' lead to 4-0.
The inning began with Gary Matthews Jr., who had just replaced Torii Hunter in center field, being charged with a three-base error after dropping Derek Jeter's fly ball on the warning track.
Jeter singled in the first, surpassing Babe Ruth for second on the Yankees' all-time hits list with 2,519. He notched a single in the seventh.
Santana gave up his lone walk of the game to Bobby Abreu before Rodriguez sent a towering shot to right-center.
Santana, who was 4-0 in his previous seven starts, lost for the first time since July 27 against Baltimore. The right-hander, moved up in the rotation because of an injury to Jered Weaver, allowed six runs and eight hits in 6 1-3 innings, striking out six. Santana had fanned seven or more batters in seven consecutive starts, the first Angel to do so since Nolan Ryan in 1978.
Angels left fielder Reggie Willits dived for a backhanded catch of Xavier Nady's double in the second, but the ball bounced off his glove, giving New York a 1-0 lead.
Damon hit a two-run homer that chased Santana in the seventh, making it 6-1. He added a solo shot in the ninth.
One night after routing the Yankees 12-1, the Angels' only run came on Vladimir Guerrero's RBI groundout in the sixth.
Notes: Hunter left the game because of a tight left quadriceps and is day-to-day. ... With Weaver still not ready to go Wednesday, RHP Dustin Moseley (1-3) will start the series finale for the Angels. ... Neither the Angels nor the Yankees heard from the commissioner's office Tuesday about possible suspensions as a result of the bench-clearing fight triggered by Hunter and Ivan Rodriguez a night earlier. Angels manager Mike Scioscia said he didn't anticipate any discipline, but Yankees skipper Joe Girardi said he thought there would be. Both men agreed the incident was minor, although Hunter and Rodriguez were both ejected. … Rodriguez didn't start Tuesday, with Chad Moeller catching Aceves since they had worked in the minors together. Girardi said Rodriguez's neck was bothering him after Hunter's hard shove sent the catcher's body lurching forward and his head snapping back. But Rodriguez denied he was in any pain.
