The jury in US District Court in Manhattan convicted Aleynikov on one count of theft of trade secrets and one of transportation of stolen property.
The Russian-born programmer worked for Goldman from May 2007 to June 2009, where he developed computer programs supporting the firm's high-frequency trading on various commodities and equities markets.
The bank acquired the HFT system - which generates millions of dollars a year in profits - for around $500 million in 1999 from Hull Trading Company.
Aleynikov quit Goldman to help develop a HFT platform for Teza Technologies, a Chicago-based start-up formed by ex-Citadel executive Mikhail Malyshev.
Prosecutors alleged that on his last day working for the bank, Aleynikov transferred "substantial portions" of Goldman Sachs's proprietary computer code for its trading platform to an outside computer server in Germany.
He encrypted the files and transferred them over the Internet and then deleted "the program he used to encrypt the files and deleted his computer's "bash history," which records the most recent commands executed on his computer".
In addition, he had already transferred "thousands of computer code files" related to the firm's proprietary trading program to his home computers during his two years working there.
He did this by e-mailing the code files from his Goldman Sachs account to his personal one and storing versions of the code files on his home computers, laptop, a flash drive and other storage devices, say prosecutors.
On 2 July Aleynikov flew to Chicago to meet Teza, taking a laptop and storage device holding Goldman proprietary code. He was arrested the following day at Newark airport.
Manhattan US Attorney Preet Bharara, says: "As today's guilty verdict demonstrates, we will use the full force of the federal law to prosecute those who steal valuable and proprietary information from their employers, whether those firms are on Wall Street or Main Street. The brazen theft of intellectual property by Sergey Aleynikov had the potential to cause serious harm to the company, and now he will pay for his crimes."
Last month a similar case saw former SocGen trader Samarth Agrawal found guilty in a trial on Manhattan for stealing the bank's trading code for use in his new hedge fund job.