The 24-year-old joins the Latics on loan after the last-gasp deal and follows the capture of Nick Powell earlier in the evening.
Shotton told the club's official website: "It's been a whirlwind evening and we only found out really late about Wigan's interest. I can't wait to get going now and meet the players.
"As soon as I spoke to the gaffer and he told me how much he wanted me, I made up my mind and now I can't wait to get started.
"The club is obviously moving forwards and the squad here is really impressive. The competition for places is intense but that is what all players need and I'm going to do everything I can to win a place in the team.
"I played a big part in the European campaign for Stoke and that's something else that's really appealing about the club.
"I just want to say a big thanks to everyone at Stoke City.
"It's a club I've been at for 16 years so it's played a huge part of my life. Who knows what will happen in the future but for now I'm a Wigan Athletic player and I can't wait to get started."
- Sports & Recreation