Shea was not included in Danny Wilson's squad for Saturday's home win against Nottingham Forest and it is understood the 24-year-old's omission was connected in part to his reaction to angry Barnsley fans the week before.
A brief club statement said: "Winger Brek Shea has returned to parent club Stoke City.
"The 24-year-old made eight appearances for the Reds after arriving on loan on New Year's Day from the Premier League club."
Barnsley issued a public apology on behalf of Shea and midfielder Stephen Dawson last week following their 5-0 defeat at derby rivals Huddersfield.
The club launched an investigation into the incident at the John Smith's Stadium when Dawson and Shea responded to a section of abusive supporters after the final whistle.
Barnsley slipped to the bottom of the table after their biggest defeat of the season and Dawson became involved in a passionate row with one supporter, while Shea is alleged to have made an offensive hand gesture.
Shea had been scheduled to return to Stoke on April 3 but has struggled to hold down a place in the starting line-up in recent weeks.