You have a problem with quoting. Try (this provides system() with multiple arguments):

system qw(perl -pib -e s/CAT/mouse/g D:\tmp\file.txt);

# Or in case you need to replace an arg with a variable, then start wi
+th:
system "perl", "-pib", "-e", "s/CAT/mouse/g", 'D:\tmp\file.txt';
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