Two spectators were removed from Montgomery Waters Meadow at half-time of the 1-0 victory over MK Dons accused of making racist gestures.
The club have now suspended three fans with immediate effect while they work with West Mercia Police to review evidence.
In a statement on Twitter, Shrewsbury Town said: "Further to the allegations of racist abuse during our game on Saturday v MK Dons, Shrewsbury Town FC have today suspended 3 supporters from attending all fixtures with immediate effect, pending the outcome of a joint Club/West Mercia Police investigation.
"As a club we have a zero tolerance policy to any forms of racism and discrimination and will be fully supporting a full investigation into the allegations."
The disappointing incident comes as Shrewsbury and all English football continue to make a stand against discrimination by taking a knee, which has been applauded by returning Town fans so far this season.
Speaking before the club made its announcement, assistant manager Aaron Wilbraham has condemned the alleged racial incident – and praised the club's swift response.
Steve Cotterill's No.2 revealed his teenage daughter was in attendance on Saturday and was aware of a disturbance in the area understood to be concerned.
The former Dons striker commended Town for a strong reaction and insisted 'everybody is together' on the fight against discrimination.
"My daughter was at the game and she didn't see anything (specifically) but she saw something going on, people being ejected, it's not something you want to see," Wilbraham said when asked about the incident and subsequent response.
"It's good that the club came out and made a statement like they did, because nobody wants to see that, it's disappointing.
"We move on, it's obviously two individuals and nobody wants to see that in the game.
"It's good the club, FA and everyone is making a stand at the moment, there are kids at the game and nobody wants to see or hear it.
"I think everybody's together on it, that's the main thing, it's sending out a good message and long may it continue."