The unanimous 3-0 decision came at the fourth and final hearing by the board on the matter, according to Assessor-Recorder Phil Ting, who argued that the archdiocese's transfer of 232 parcels of property from two of its nonprofit incorporated entities to a third in April 2008 was not exempt from tax.
The archdiocese argued it should not have to pay because the transfers were part of an internal restructuring.
Ting maintained that the corporations, as separate, legal entities, were required to pay transfer taxes.
The properties included vacant lots, parking lots, apartments, commercial buildings, parishes and schools throughout the city worth nearly $2 billion, according to Ting's office.
Such transfers are often made by corporations in order to protect their assets from litigation, Ting's office said.
The transfer tax, unlike the annual property tax, is a one-time, local tax.
Ting said in a statement Monday that the money owed is the second-largest transfer tax in San Francisco's history.
He said today that he was pleased with the board's "fair" decision.
"The decision clearly states that we followed the law," Ting said, adding, "We want to treat every taxpayer, large or small, the same."
The money would help the city make up its estimated $522 million deficit for the coming fiscal year, but is unlikely to be available anytime soon, as the archdiocese plans to challenge the decision in San Francisco Superior Court.
The archdiocese responded to Monday's decision with a statement saying that while it is disappointed by the board's decision, the city's property transfer law "is overwhelmingly in favor of the Archdiocese."
The archdiocese said the board "apparently faced a tremendous amount of pressure in view of the city's desperate need for revenue."
The statement also accused Ting's office of "inexcusable delays and, at times, arrogance."
"Therefore, we are glad that having exhausted the required administrative process we can finally proceed to a formal, neutral civil court forum," the archdiocese said.
Ting responded today by noting the archdiocese's nonprofit status.
"Unfortunately, this is a taxpayer that's not used to paying taxes, and they are upset that we made this decision," he said.
Ting said he was not surprised the archdiocese would move the case to court and that the city is prepared to defend his office's decision.