I am not sure that it's useful to perform the intermediate step of substitution. This ought to work:

my @searchWords = split(/\s+/, $Input{'query'});

foreach my $active(@active){
    my $newd = lc($active);

    foreach my $searchWord(@searchWords){
        $searchWord = lc($searchWord);
        push(@found, "$active:  matches '$searchWord'") if grep { /$se
+archWord/ } $newd;
    }
}

__END__
prints "active: matches searchWord"
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