Including a 13-0 whitewash Sunday at Houston, the Yankees have tossed consecutive shutouts for the first time since May 7-8, 2005, against Oakland.
Pettitte (7-5) tied a season high with nine strikeouts in seven innings, improving to 4-0 in his past six starts. He allowed five hits and walked one, passing former pitching coach Ron Guidry for fourth place on the franchise list with his 171st win for the Yankees.
Coincidentally, it was the 30th anniversary of Guidry's 18-strikeout game against the California Angels at Yankee Stadium, a club record.
Pettitte, who owns a 208-118 career mark, has allowed one run over 15 innings in his past two starts since giving up 10 in a no-decision against Kansas City on June 7.
The Padres brought about 150 extra people in their traveling party, mostly front-office staff and invited guests, so they could visit Yankee Stadium in the storied ballpark's final season.
But San Diego played a messy game in this 1998 World Series rematch, throwing two wild pitches and committing three errors - two by fill-in second baseman Craig Stansberry.
The Padres also recalled prized prospect Chase Headley from the minors. Headley made an error in left field and finished 2-for-4 as San Diego lost for the fourth time in 12 games.
Rodriguez homered to center leading off the second, his 13th this season and No. 531 career. Giambi connected one batter later and added a two-run shot in the fourth after a leadoff walk to Hideki Matsui.
Giambi has 17 home runs this year and 37 career multihomer games.
The Yankees tacked on three more runs in the fourth off Wolf (5-5), making his first career appearance at Yankee Stadium in his 10th major league season.
The left-hander entered 3-0 with a 1.91 ERA in his past five starts, but lasted only four innings. He was tagged for seven runs - five earned - and six hits.
It was the first time Wolf served up three homers in a game since April 29, 2005, with Philadelphia.
Giambi was lifted for pinch-hitter Wilson Betemit in the seventh. Derek Jeter finished with two RBIs.
Jose Veras, Billy Traber and Mariano Rivera (three strikeouts) completed the seven-hitter, New York's fifth shutout this season.
San Diego was blanked for the fifth time.
