Shotton has made over 60 appearances for Stoke, but has not featured since Mark Hughes replaced Tony Pulis as manager in the summer.
He has previously taken in loan spells at Altrincham, Tranmere and Barnsley, and has now linked up with Championship club Wigan.
The 24-year-old's move was finalised just two minutes before the 11pm deadline and he is looking forward to his time at the DW Stadium.
"It's been a whirlwind evening and we only found out really late about Wigan's interest," Shotton told the club's official website. "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."