Armed officers swooped on Lifestyle Express in Rockingham Road, Wheatley, after being called to a report of a man armed with a gun inside the shop.
An armed police officer fired their weapon during Monday’s confrontation.
The suspect, 27, was injured in the shooting. He was taken to hospital where he remains in a stable condition.
He has since been arrested on suspicion of possession of a firearm with intent to endanger life.
The shooting has been referred to the Independent Office for Police Conduct.
South Yorkshire Police Assistant Chief Constable Richard Alton said: “We know that this morning’s incident will have no doubt caused some serious concern, especially among those living nearby.
“I’d like to stress that we’re taking this morning’s events extremely seriously and we are working alongside the Independent Office for Police Conduct to unpick exactly what happened.
“There will be a number of officers at the scene today carrying out enquiries as our investigation continues.”
Anyone with information can report it online at our online portal on our website at www.smartcontact.southyorkshire.police.uk or by calling 101.