Visitors' hands are stamped with entry seals so as to distinguish them from jail inmates, but the two children were stamped on the face.
"We have suspended prison guard Rashmi Prajapati," Director General (Jails) Sanjay Chowdhary said.
"It was found that she stamped their faces with entry seals, but it was done without any malicious intention," he said, adding that a departmental inquiry has been ordered.
Bhopal Central Jail's Superintendent Dinesh Nargave had said the stamping of faces may have taken place due to rush of visitors that day.