The popular Mexican had the bulk of the arena supporting him but that same crowd were booing by the end when the scorecards were read out.
Most ringside observers had Vera winning the fight but judges Gwen Adair (98-92), Carla Caiz (97-93) and Dr. Lou Moret (96-94) unanimously called the fight in favour of Chavez.
Kevin Iole of Yahoo! Sports, Dan Rafael of ESPN and former judge turned HBO analyst Steve Weisfeld all scored the fight 96-94 in favour of the Vera.
The Compubox punch stats showed that Vera landed with 176 of his 734 punches while Chavez landed 125 punches from just 328 thrown.
The fight comes in the wake of recent judging scandals involving Floyd Mayweather and Ricky Burns.
Mayweather was denied a unanimous decision against Canelo Alvarez two weeks ago when judge CJ Ross somehow saw his one-sided victory as a draw. Ross stepped down in the wake of the storm that followed.
Also earlier this month, Ricky Burns kept his WBO world lightweight title in Glasgow after a hugely controversial draw against Mexico’s Raymundo Beltran that was seen by most as a 'hometown decision.'
Vera's promoter Artie Pelullo was disgusted with the scorecards in LA: "The one judge had it 98-92, which basically means that Bryan Vera wasn't even in the fight and they didn't give him credit for a thing he did," he is quoted as saying by Yahoo! Sports.
"They gave him no credit for the quality of the fight that he had. It's like he didn't exist. It's unbelievable. I told the commissioner [Andy Foster, of the California State Athletic Commission], 'A judge in Nevada lost her job for doing this kind of thing.' 98-92? 97-93? What are you watching?
"You know me and I don't get crazy, but that was a travesty. He won that fight. If he lost the fight by one point, OK. I don't agree, but OK. But he didn't lose the fight by one point. According to them, he wasn't even in the fight."
Chavez who weighed in at 172.4 pounds but entered the ring closer to 190, shrugged off the criticism.
"I was very close to knocking him out three times in the fight," he said.
"One of the rounds, he was really hurt and it should have been a 10-8 round."
Chavez's legendary father, who was training his son for the first time, also scoffed at Vera's performance.
"I know about boxing and have been in this sport all of my life," Chavez Sr said. "Who connected the best punches? When Bryan Vera did anything against Julio, it was because he was hitting him low and using his head. That's all he did."
Vera for his part said he did everything he could: "This was the best performance of my life. The weight was never an issue. The gameplan was exactly what we did. I had to take some of the macho-ness out and I was never hurt during the fight."