The Munster forward was sent off in the 22nd minute for a tackle on Springboks fly-half Pat Lambie and could be hit with a suspension after being cited for the challenge.
However, Schmidt has suggested that the tackle was not reckless as it initially looked.
He is quoted by PA as saying: "CJ's got both hands extended, once you're in the air you can't change your trajectory.
"CJ was upset that Pat was hurt as much as he was upset that he had to leave the field. It's one of those things that happens."
Despite Stander's red card, Ireland went on to record a first Test victory in South Africa, winning 26-20 in Cape Town.