Goals to Newcastle strikers Sasho Petrovski and Labinot Haliti in front of 23,317 fans came after US international Landon Donovan put the Galaxy ahead in the eighth minute.
Beckham, who in 2007 thrilled a sold-out former Olympic Stadium with a trademark free kick in a 5-3 loss to Sydney FC in his last trip Down Under, almost repeated the effort with a powerful shot on the stroke of halftime against Newcastle. But his shot sailed just across the face of goal.
The former Manchester United and Real Madrid star shrugged off the miss: "Some go in, some don't. Maybe in another game." Beckham started the sequence that led to Donovan's goal.
His pass found striker Edson Buddle, who combined with Chris Birchall before Sean Franklin whipped in a dangerous cross.
Jets defender Taylor Regan and inexperienced goalkeeper Matthew Nash both missed the ball in a mix-up, allowing Donovan the easiest of finishes to score.
The Galaxy should have doubled the lead minutes later when a long-range shot from Juninho struck the underside of the bar and appeared to cross the line, but was not awarded.
Galaxy coach Bruce Arena praised Beckham after the match, saying the English star wasn't fit to play but insisted he wanted to stay on.
Beckham, who has also battled a groin problem in recent weeks, said he always wanted to play.
"I normally wouldn't have played but I think when a game like this comes up you want to play," Beckham said.
"Tonight was tough obviously, getting myself fit for it.
"I haven't trained since our last game but aside from the back pain, I enjoyed the game ... the majority of time I was pain free." Beckham said he was impressed by the quality of the Jets, saying he hoped to return to secure a win over Australian opposition.
"Maybe third time lucky," Beckham said. "It's obviously disappointing to lose the game tonight but we'll be back." At the end of the match, Beckham handed his shirt to a female fan in the crowd. He later sent a shirt to Newcastle captain Kasey Wehrman.
