But your program will miss the last empty field. In 1|2||3|45|||6|, for example, your program stops too early:

.
.
NEW: 45
NEW:
NEW:
NEW: 6
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(One empty NEW: line should follow, since separators separate fields, rather than terminate them.)

If that were the only issue, you could just append a single '|' to the input string before the rest of your logic.

The second problem, though, is that your regex converts empty fields to a single space ' '. True, you could easily replace them, but if the field was ' ' in the first place, the value will be destroyed. That may not be a problem depending on the data, but to fix this, and the previous issue, you can make a couple of changes:

$line =~ s!\|!\| !g;
.
.
@new = map { substr $_, 1 } split /\|/, $line;
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Or, as the OP suggested he was trying to avoid, he could just add a non-blank field to the end. In that case the entire code reduces to:

my @new = split /\|/, $line . '|sentinel';
$#new--; # Remove sentinel
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But of course, split /\|/, $line, -1; still gets my vote. :-)