Amphetamines are considered a performance-enhancing substance and are in violation of the Minor League Drug Prevention and Treatment Program.
The suspension of Hernandez will be effective at the start of next season.
"We strongly believe in the Commissioner's drug-testing program, and we are disappointed in the choice that Runelvys made," Astros general manager Ed Wade said. "Major League Baseball and the 30 clubs have taken great strides toward eliminating the use of performance-enhancing substances in baseball, and we are fully supportive of all measures to ensure a clean game."
Hernandez was 0-3 with an 8.38 ERA for the Astros this year, allowing 18 earned runs over 19 1/3 innings. He was with the Astros two separate times, with his most recent demotion arriving on July 28, when the club activated Roy Oswalt from the disabled list.
Alyson Footer is a reporter for MLB.com. This story was not subject to the approval of Major League Baseball or its clubs.