They don't, I don't think. They contacted the providers directly and asked them to do it. They don't just have a magical pull-switch - they just have phones, and apparently a lot of pull.
According to Fairow, the statement from BART saying that cell carriers participated in the shutoff isn't precisely it. Fairow says that language in BART's contract with carriers allows BART to "flip a switch" to cut off service for issues of safety. A spokesperson from one of SF's major wireless carriers confirms this, and says that the carriers themselves weren't involved in the shutdown.
"Ultimately, I'm the one that implemented it," said Fairow. "It was certainly run through through channels. A lot of thought went into this."
Source: http://sfappeal.com/news/2011/08/bart-cell-fcc.php
All of the reports that I have seen (including the CNet story linked above) have retracted any statement that the wireless carriers turned off the signal at BART's request.
The bigger issue to me is that is almost certainly illegal to willfully disrupt 911 service, and it's unlikely that whoever flipped whatever switch, be it disrupting commercial power to carrier-owned base stations or a BART-owned DAS, was able to disrupt texts/voice calls to other parties selectively without disrupting 911 service.
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