Bauer joined the English club from Rubin Kazan in the January transfer window, and made 15 Premier League appearances in the second half of the 2017-18 campaign.
A number of players have been linked with moves away from Stoke following their relegation to the Championship, but Bauer has penned a new long-term deal at the bet365 Stadium.
"I've never made any secret of how much I have enjoyed my time with the club since joining in January," Bauer told the club's official website.
"I have been made to feel so welcome by people at the club and people in the city and that means a great deal. The way last season ended was bitterly disappointing for all us but I want to be part of the squad that helps Stoke City back into the Premier League.
"As a person and a player I love a challenge and I'm excited about what lies ahead for us."
The 26-year-old had initially signed a four-and-a-half-year contract upon his arrival in the early stages of 2018.