Somewhat unrelated to the question, but please, please do use here documents.

foreach $table (@tables) {
    chomp $table;
    print OUTFILE <<"EOT";
BEGIN
   DBMS_REPCAT.CREATE_MASTER_REPOBJECT (
      gname => 'beastdb_mstr_grp',
      type => 'TABLE',
      oname => '$table',
      sname => '$schema',
      use_existing_object => TRUE,
      copy_rows => FALSE);
END;
/

EOT
}
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Also, there's no reason to slurp the entire input file here.

open (INFILE, "< $infile") or die "Couldn't open $infile: $!";
open (OUTFILE, "> $outfile") or die "Couldn't open $outfile: $!";

chomp, print OUTFILE <<"EOT" while <INFILE>; # shorter version
BEGIN
   DBMS_REPCAT.CREATE_MASTER_REPOBJECT (
      gname => 'beastdb_mstr_grp',
      type => 'TABLE',
      oname => '$_',
      sname => '$schema',
      use_existing_object => TRUE,
      copy_rows => FALSE);
END;
/

EOT

close (INFILE);
close (OUTFILE);
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Update: If that looks too strange, you might want to do something like:

foreach $table (@tables) {
    print OUTFILE (map "$_\n",
        "BEGIN",
        "   DBMS_REPCAT.CREATE_MASTER_REPOBJECT (",
        "      gname => 'beastdb_mstr_grp',",
        "      type => 'TABLE',",
        "      oname => '$table',",
        "      sname => '$schema',",
        "      use_existing_object => TRUE,",
        "      copy_rows => FALSE);",
        "END;",
        "/\n",
    );
}
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