Last Friday's 0-0 draw saw Real Madrid star Bale booked for a high tackle on O'Shea, earning him a suspension for his country's game against Serbia in June, shortly before Neil Taylor was shown a red card for a challenge which broke Seamus Coleman's leg.
The forward protested his booking on the pitch and after the match but Ireland defender O'Shea was critical, insisting he had been lucky to avoid a more serious injury than the stitches required to his shin.
O'Shea felt the Bale was fortunate not to see red and O'Neill was in agreement, condemning that tackle as well as the heavy challenge by Taylor which left Coleman with a double leg fracture.
"I have seen the challenge on Seamus and I have seen the challenge on John O'Shea - they are very poor challenges," O'Neill told BBC Sport.
Coleman has undergone surgery and O'Neill provided an update on his condition.
"He was taken to hospital on Friday night, he was very groggy," said the Ireland manager. "He had the operation on Saturday morning and that was successful.
"Naturally, he is very disappointed. It will take some time to heal. It is a double break but it has been pinned up and screwed in place.
"The doctors are very pleased with the way the operation has gone. Now, it is time for recuperation.
"Seamus has great determination and sometimes things works very well in your favour in terms of recovery.
"He has been phenomenal at his club and for us as captain of our team. It is a devastating blow for the lad.
"Even the doctors and surgeons wouldn't be sure at the moment [about the recovery time]. Sometimes there can be complications, other times it can be clear and it is all plain sailing."