Heaton impressed despite Cardiff's 4-0 defeat at Arsenal on Monday night after reclaiming his place in the team following an injury to Peter Enckelman.
However, he complained of a thigh problem and scans back at parent club Manchester United have resulted in a five-week absence for Heaton.
"I'm absolutely gutted," said Heaton in the South Wales Echo. "One minute you are OK and you get your chance, the next this happens and you're out for five weeks.
"It's so frustrating because I've had to wait for my chance and now this happens, but we have talked about mental strength at the club and that's been important to me in the last couple of months.
"And I've got to be strong now because this is one of those things that happens in football."
With Heaton and Enckelman sidelined, recent loan signing Dimi Konstantopoulos is likely to start Sunday's Championship clash with Wolves.