Russian Aleksandr Andreevich Panin has been sentenced to nine-and-a-half years in jail. His accomplice, Algerian Hamza Bendelladj, will serve 15 years.
They created the SpyEye virus package that is believed to have infected more than 50 million computers.
The sophisticated malware could steal sensitive data or let hackers use infected machines to send spam.
The pair used SpyEye themselves but also offered it as a malware "kit" to anyone willing to pay for it, said the US Department of Justice (DoJ). The most sophisticated version of SpyEye cost about $10,000.
Once large numbers of PCs were infected with SpyEye, the pair ran tools that siphoned off cash and also helped the malware spread further.
Cleaning up the damage caused by SpyEye from 2010 to 2012 is believed to have cost banks around the world more than $1bn, said the DoJ.
"It is difficult to overstate the significance of this case, not only in terms of bringing two prolific computer hackers to justice, but also in disrupting and preventing immeasurable financial losses to individuals and the financial industry around the world," said US attorney John Horn in a statement.
"The sentences that were imposed reflect the magnitude of the harm," said Mr Horn.
Panin, known as "Gribodemon" and "Harderman" online, pleaded guilty to bank and wire fraud charges in January 2014 after reaching a deal with prosecutors.
"I want everyone in this courtroom to understand my actions were inexcusable and inexplicable," said Panin at the sentencing hearing. Panin was arrested in 2013 as he passed through Atlanta, Georgia on an international flight.
Bendelladj, known as Bx1 online, also pleaded guilty but has not reached a deal with prosecutors. His lawyer said he planned to appeal.
Bendelladj was arrested in Bangkok, Thailand in early 2013 while changing planes and was extradited to the US shortly afterwards.
Tackling SpyEye helped law enforcement officers shut down a notorious malware marketplace called Darkode.com, said prosecutor Steven Grimberg.
Panin and Bendelladj were "legends" in the criminal underworld, said Mr Grimberg, adding that the sentences would send a message to other cybercriminals.
Computer hackers who created malware that stole about $100m (£70m) have been given long jail sentences in the US.