The United States winger helped set up Michael Kightly's opener and then scored the second inside the first 20 minutes before his night ended with a first-half challenge from Matt Kassel.
Shea, who had only just joined up with his teammates after a successful Gold cup campaign with the USA, limped off the field and used crutches while speaking to reporters.
He said: "Obviously I'm pretty upset right now. I was excited to get back to Stoke and get ready for the season. Hopefully it's not as bad as it feels."
Manager Mark Hughes was fuming about the incident and reckons Shea, who will undergo an MRI scan on Wednesday to assess the damage, will be out for a "number of weeks at least".
Hughes said: "It was a nasty injury. It looks like some damage to the ligaments in his knee. He's going to be scanned. I thought it was a very, very poor challenge by the boy. What the hell was he was thinking of, I have no idea.
"It's a friendly game. You need to protect your fellow professional. And I don't think the guy did that. I don't know who he was. Maybe he was trying to make a name for himself, I don't know. He went the wrong way about it."
However, Shea defended the challenge made by Kassel, who was booed by some of his own supporters during the game.
He said: "He was going for the ball. I tried to put my body in front of his and it's soccer. Tackles happen - good and bad. I've done worse to other people. I'm not mad at all.
"When I was walking off, he apologized."
Right-back Kassel, who has only played 33 minutes for the Union this season and was part of a starting line-up made up entirely of reserve players, insisted he did not mean to harm the 23-year-old winger.
"Obviously I didn't mean to do that," Kassel said. "I'm friends with the kid. It was completely just going for the ball. Unfortunately things happen and tonight he unfortunately got hurt.
"There was no intent at all. I wish him all the best and I apologize for the tackle."
Stoke kick off their Premier League campaign at Liverpool on August 17.