The judge's ruling clears the way for Governor Brown's tax initiative to be placed at the top of the November ballot thanks to a state budget that orders bonds and Constitutional amendments, like Brown's, be listed first.
Political experts believe the move will give the governor an advantage because voters are more likely to mark "yes" on measures that are higher up.
"It deserves the dignity of being ranked with other Constitutional measures and bond issues," said Brown.
A competing tax measure from the group, Our Children, Our Future and financed by wealthy civil rights attorney Molly Munger, argued they submitted their organization signatures before the governor did and therefore should be placed ahead of his measure.
Rather than argue the validity of the budget move, attorneys for the governor's rival criticized Los Angeles County elections officials for hanging on to their initiative while three other measures submitted days apart were also certified. All four were turned in to the secretary of state at the same time.
"You can't just sit and then do them all at once because that's what's convenient," said Bradley Phillips, Munger's attorney, in court.
But the judge was reluctant to tell counties how to run their operations.
"Aren't you asking me to essentially micromanage the registrar's office?" said the judge.
Our Children, Our Future decided not to appeal the loss because they say it doesn't matter where they are on the ballot.
"Look, the deck may be stacked against us, but we've got a good ballot measure here that's actually going to help California schools, and we're going to fight for it, and we believe we're going to win in November," said Nathan Ballard, spokesman for Our Children, Our Future.
The governor's victory, though, may be short-lived. The Howard Jarvis Taxpayers Association appealed the ruling and argues the state budget shouldn't dictate the position of a ballot measure.
"The ability of the legislature to pervert the election process, and I think that's what's at issue here," said Jon Coupal, president of the Howard Jarvis Taxpayers Association.
Counties need a decision soon, as the secretary of state needs to get the November ballot to the printers soon. Ballots to California military members stationed overseas must be mailed in two months.