The Citadel network had remotely installed a keylogging program on about five million machines to steal data.
About 1,000 of the 1,400 or so networks that made up the Citadel botnet are believed to have been shut down.
Co-ordinated action in 80 countries by police forces, tech firms and banking bodies helped to disrupt the network.
"The bad guys will feel the punch in the gut," Richard Boscovich, a spokesman for Microsoft's digital crimes unit said.
The cybercriminals behind Citadel cashed in by using login and password details for online bank accounts stolen from compromised computers.
This method was used to steal cash from a huge number of banks including American Express, Bank of America, PayPal, HSBC, Royal Bank of Canada and Wells Fargo.
Citadel emerged after core computer code for a widely used cybercrime kit, called Zeus, was released online.
Underground coders banded together to turn that code into a separate cybercrime toolkit that quickly proved popular with many malicious hackers.
In a blogpost detailing its action
, Microsoft said Citadel had also grown because malicious code that could take over a PC had been bundled in with pirated versions of Windows.
The millions of PCs in the criminal network were spread around the globe, but were most heavily concentrated in North America, Western Europe, Hong Kong, India and Australia.
Despite the widespread action, which involved seizures of servers that co-ordinated the running of Citadel, the identity of the botnet's main controller is unknown.
However, Microsoft has started a "John Doe" lawsuit against the anonymous controller, believing him to use the nickname Aquabox and be based in Eastern Europe.
In addition, the FBI is working with Europol and police forces in many other countries to track down and identify the 81 "lieutenants" that helped Aquabox keep Citadel running.
Microsoft has also started action to help people clean up an infected computer.
Typically, it said, machines compromised by Citadel were blocked from getting security updates to ensure those computers stayed part of the botnet.
With the network disrupted, machines should be free to get updates and purge the Citadel malware from their system.