The Bluebirds unveiled the kit for their maiden season in the Premier League on Wednesday which included shorts in a slightly deeper shade of red than the shirts and socks.
However, after fans expressed their displeasure on various social media sites, the club decided to allow season ticket holders to vote on the design.
Cardiff's home kit during their Championship title-winning campaign included black shorts, and that proved the most popular option with the fans who voted.
A statement on the Cardiff website read: "It's a decision that Tan Sri Vincent Tan and all at the club fully supports, and we will next instruct Puma to work on supplying the shorts as soon as possible.
"Once again, we thank all supporters who took the time to vote."
The club made the controversial switch from their traditional blue kit to red under owner Tan at the start of last season, while the club crest was also heavily altered.