The governor's line-item cuts were spread among health, education, transportation and natural resources.
He also vetoed $366 million for the CalWORKS Welfare-to-Work program and $256 million for subsidized childcare.
Lawmakers were in session all night Thursday.
Three democrats who can normally be counted on for yes votes were withholding mainly because of years of cuts, including this year's $7.5 billion, which were just too much to bear.
In the end, many lawmakers called the budget an imperfect compromise, but they expressed relief that the 100-day stalemate was finally over.
"I'm proud to say that we Democrats and Republicans fought through all of the minefields and all of the obstacles that were in front of us and we got the job done," said Schwarzenegger on Friday.
"It just seems like when everybody's struggling so hard to pay their bills and make ends meet, this is the worst possible thing you could do. It hurts families, it cuts jobs, and it makes it harder for people to go to work," said Nancy Berlin with California Partnerships
Berlin accused the governor of using his veto to undo the budget compromise that was reached.
Schwarzenegger's line-item veto cut $52 million to HIV and AIDS programs. The money would have restored critical funding lost last year when the governor slashed more than $85 million from those programs.
"We've become one of the few states that doesn't support HIV prevention, surveillance or home-based care," said Craig Thompson of AIDS Project Los Angeles. "It's really tragic."
Thompson said the loss in funding will likely cause a spike in the number of HIV and AIDS cases in California.
A measure that also passed in the budget was one that will go before voters in 2012 to bolster the state's rainy day fund and cut back pension benefits for new state workers.
The state controller will now analyze the state budget to see if there's enough money to pay $8 billion of overdue bills.