for my $i (0 .. $#array) {
    substr($string, $i, 1) = lc substr($string, $i, 1)
        if $array[$i] eq q();
}
[download]

Update: As always, TIMTOWTDI...

$altered_string =
    join q(),
    map {
        my $char = substr($string, $_, 1);
        $array[$_] eq q() ? lc($char) : $char;
    }
    0 .. length $string;
[download]