Francisco Rodriguez pitched a scoreless ninth for his major league-leading 30th save in 32 opportunities.
Cole Hamels (7-5) gave up three runs and six hits in seven innings for the Phillies, who have lost five straight and seven of nine.
Philadelphia has lost four straight series since it swept the Braves in Atlanta.
The Angels pushed across three runs in the second inning. Vladimir Guerrero led off with a single, extending his hitting streak to 13 games. Guerrero moved up on Torii Hunter's groundout and scored when Gary Matthews Jr. singled to center.
Kotchman followed Matthews with a two-run drive to right to make it 3-0. It was Kotchman's eighth homer of the season.
The Phillies cut it to 3-1 in the third. Chase Utley snapped an 0-for-24 skid with a two-out double to right-center and scored on Ryan Howard's base hit.
Jimmy Rollins stole a pair of bases in the first, giving the reigning NL Most Valuable Player a major league-best 31 consecutive steals, dating to last season. Rollins has 17 stolen bases this season.
Rollins also had an RBI double in the seventh.
