Perdomo replaces Cardinals pitching prospect Alex Reyes (St. Louis' No. 3 prospect), who also has been dealing with a shoulder issue.
The Futures Game takes place at 3 p.m. ET on Sunday at Great American Ball Park, and it will be broadcast live on MLB Network and MLB.com.
Cash Kruth is a reporter for MLB.com. Follow him on Twitter at @cashkruth. This story was not subject to the approval of Major League Baseball or its clubs.