The midfielder was due to remain with Barnsley until April 3, but has not featured since making an offensive gesture to a fan and his loan spell has since been terminated
The United States international made eight appearances for relegation-threatened Barnsley, the last of which was shrouded in controversy.
Shea made an offensive gesture towards Barnsley fans following their 5-0 defeat to Huddersfield Town earlier this month in what has proven to be his last appearance for the Oakwell outfit.
The 24-year-old midfielder apologised for his behaviour but it appears as though his indiscretion has cost him a chance to impress.
"I would like to unreservedly apologise for what happened at the end of the match," he tweeted in the week after the Huddersfield loss.
"Although my actions were aimed at one person who was abusing a team-mate, I realise I should not have reacted in that way in the heat of the moment."
However, after missing Barnsley's 1-0 win over Nottingham Forest the club confirmed that Shea, whose loan deal was due to run until April 3, had returned to his parent club.
Shea has played in three Premier League games for Stoke since arriving in January 2013, but has yet to start a league match.