If you read further in the article you'll hit >The FBI worked with a number of security researchers to reverse engineer the DGA and figure out how it generated

If you read further in the article you'll hit >The FBI worked with a number of security researchers to reverse engineer the DGA and figure out how it generated the list of domain names it provided to the infected computers every week. That way, the FBI would know which thousand domains were being selected every week in advance. Then, right before the takedown, they acquired a temporary restraining order that required domain registries in the U.S. to redirect any attempts to contact those thousand domains to a substitute, government-run server. So the answer is, yes, there was a way, and so eventually that's what law enforcement did.