It was "sinkholed" by registering, suspending or seizing all domain names with which the malware could communicate, and redirecting all traffic.
The operation is believed to have halted the botnet before it could infect millions of computers which was a bit of a worry because the malware is particularly clever.
Beebone can change its identity by downloading different versions of itself to avoid traditional signature-based antimalware detection methods.
According to security researchers, there are over 5 million unique W32/Worm-AAEH samples, with more than 205,000 samples from 23,000 systems in 2013-2014.
Europol's deputy director of operations, Wil van Gemert, said the operation showed the importance of international law enforcement working together with private industry to fight the global threat of cyber crime.
"We will continue our efforts to take down botnets and disrupt the core infrastructures used by cyber criminals to carry out a variety of crimes. Together with the EU member states and partners around the globe, our aim is to protect people worldwide against these criminal activities."