The left-hander hadn't allowed a runner past first base until running into trouble with two outs in the seventh. But the Angels quickly answered off Brett Myers.
Chone Figgins singled with two outs and Aybar followed with a drive to right field for his third career homer in 393 at-bats. Aybar entered the game in the third inning because shortstop Maicer Izturis left with tightness in his right hamstring.
The Angels have won the first two games in this interleague matchup of division leaders. Since sweeping a three-game series in Atlanta earlier this month, the Phillies are 3-8, including their first four-game losing streak of the season.
Scot Shields struck out four batters in the eighth, including Ryan Howard to leave two runners on. Shane Victorino reached on a wild pitch after he fanned with two outs.
Francisco Rodriguez entered with two on in the ninth and got the last three outs for his 29th save in 31 chances.
Jayson Werth broke Saunders' bid for his first career shutout with a solo shot to center in the seventh. Angels center fielder Gary Matthews Jr. drifted back for the ball and appeared to have it lined up a few feet in front of the warning track. He suddenly turned around and watched it clear the wall and bounce back onto the field.
Chris Coste followed with a walk and scored on Pedro Feliz's double to left-center to tie it at 2. Eric Bruntlett then singled to center, but he was thrown out going to second after Feliz was held up at third.
Guerrero gave the Angels a 1-0 lead in the fourth. He drove another one to left-center about one section away from his first shot to make it 2-0 in the seventh.
Guerrero tormented the Phillies when he played for the Montreal Expos, and he's doing it again now in his fifth season with the Angels. He has 31 homers and 84 RBIs against Philadelphia, most against any team in both categories.
Myers, awful as a starter this season after a successful stint as a closer last year, had one of his better outings. He allowed four runs and six hits in 7 2-3 innings, but was hurt by the longball as usual. He's given up a major league-leading 23 homers.
Saunders was originally drafted out of high school by the Phillies in the fifth round of the 1999 amateur draft. He didn't sign a contract, went to Virginia Tech and was selected in the first round (12th overall) by the Angels in 2002.
The slumping Chase Utley got a rare night off for the Phillies. He's second in the majors with 22 homers, but is hitless in his last 23 at-bats and is hitting .158 in his past 15 games.
Notes: Guerrero has 35 career multihomer games, including two this season. ... Utley had started 101 consecutive games. ... The Phillies are 2-6 in interleague play.