"We're happily surprised," campaign spokesman Jon Golinger said.
He said the vote shows that residents care about "protecting our beautiful waterfront."
Before the election there was mounting pressure from opponents, which included the San Francisco Chamber of Commerce and San Francisco Labor Council and other labor and planning groups, to keep the status quo for development projects.
The No on B campaign argued that voters already have the power to oppose projects and that the initiative sets a "dangerous" precedent for other planning projects throughout the city.
More than 40 percent of voters opposed the measure, which surpassed the majority vote required to pass.
According to Golinger, with the measure's passage most future plans for the waterfront will comply with established rules and height limits.
"It's the really rare exception that will have to go to the voters," he said.
One such project that he anticipates will be on the November ballot following Measure B's unofficial passage is plans for Pier 70 by San Francisco-based real estate company Forest City.
The preliminary plan calls for a mixed-use housing complex with one building reaching at least 80 feet, which is above the limits for that section of the waterfront.
Measure A, an earthquake safety and emergency response bond measure, passed with about 80 percent support. The initiative will use $400 million in bonds to go toward public safety and emergency response purposes.
With the measure's approval, the funding would be solely used to improve and fix the emergency firefighting water system and other facilities, upgrade police and fire stations, and build a seismically safe building for the medical examiner, the police motorcycle unit and crime lab.
Those facilities are not considered safe in the event of an earthquake or major disaster and need to be brought up to building code.