Shinnie joined the Millers at the end of January 2016 under former Rotherham boss Neil Redfearn.
However, the subsequent appointment of Neil Warnock as Redfearn's replacement just two weeks later saw 26-year-old Shinnie's chances with the Championship side limited and he made just three appearances during his spell at the New York Stadium.
Johnstone spent the whole of the 2015/16 season at Scottish Championship side Greenock Morton.
It was a successful campaign for the 21-year-old, who made 43 appearances and scored 17 goals for the Ton as they finished in fifth place.
Meanwhile, Blues can confirm that Ryan Shotton, Kyle Lafferty and Will Buckley have returned to their parent clubs Derby County, Norwich City and Sunderland respectively, after finishing their loan at St. Andrew's.
Defender Shotton, made nine appearances for Gary Rowett's side, with Northen Ireland Lafferty turning out six times and winger Buckley 10 times.
Birmingham City would like to thank all three players for their contribution and wish them every success in their future careers.