Assembly Bill 110 was approved 28-10 in the Senate and 54-25 in the Assembly, hewing to party lines in both Democrat-controlled houses.
A balanced budget was due by midnight Saturday. A deal was reached earlier in the week, prompting swift action Friday.
Republicans and Democrats disagreed over whether the budget will further California's recovery or return it to large deficits seen during the last recession.
Republicans contend the spending plan contains accounting gimmicks and fails to address some of the state's most pressing fiscal time bombs, including tens of billions of dollars in unfunded public employee pension liabilities.
Democratic lawmakers said they did not get the spending restorations they sought because the leadership agreed to go with the governor's more conservative estimates of tax revenue in the coming fiscal year. They favor a revenue estimate offered by the nonpartisan Legislative Analyst's Office, which was $3.2 billion higher.
The budget funnels significantly more money to K-12 schools and alters the education funding formula so more money will flow to district with high levels of students who come from low-income families, who are not proficient in English or who are foster children. The funding shift was one of Brown's top legislative priorities of the year.
Thanks to a recent voter-approved initiative, Democrats could pass the budget on a simple majority vote and did not need Republicans' support. Democrats noted the budget maintains a roughly $1 billion reserve and will not restore all the programs cut during the recession.
The Associated Press contributed to this report.