The Mets had scored on a Timo Perez RBI single in the first that plated Mike Piazza (it also appeared to plate Jason Phillips, playing in front of friends and family in San Diego, but home plate umpire Chuck Meriwether blew the call at the plate, ruling that Phillips had been tagged out by catcher Gary Bennett on a relay throw from Mark Kotsay) and a Marco Scutaro solo homer in the fifth.
San Diego (48-78) scored their first run in the bottom of the third on Mark Kotsay's triple down the right field line that brought home Kevin Jarvis.
Stanton walked Mark Lorretta on a 3-2 pitch, and then proceeded to deny Glavine his 251st career victory by serving up a Phil Nevin homerun over the rightfield wall. Visibly upset, Stanton retired the next two Padres, but the damage had been done.
Scott Linebrink (2-2) pitched a scoreless eighth to earn the victory.
Rod Beck pitched a perfect ninth to notch his seventeenth save of the season.
New York (54-70) had only seven hits in the contest.
Kevin Jarvis -- who entered having lost each of his previous three starts -- tossed seven innings, allowing seven hits and two runs while walking two and not striking out a batter.