Your C-style for loop runs from zero to minus one, because $#efile refers to the last index of the array @efile, which is created on the spot - empty. Your task will be much simpler if it is written using the idiomatic $_ variable.

#!/usr/bin/perl

use warnings;
use strict;

my $input_file = 'dump.vcd';

open (INPUT, '<', $input_file)
    or die $!;

while (<INPUT>) {
    s/\$var\w \d+ ([!,\#,\",\$,\%,&]) (\w) \$end/\$var $1 $2/;
    print;
}

close INPUT;
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That has the benefit that the file is read and processed one line at a time, with no space taken for an array to hold it. I added warnings and strict, which would have told you what was wrong. I also improved open to the 3-arg form and added error checking in case open fails.

I don't believe your character class is exactly what you think it is because of all the commas and escapes. I didn't modify the s/// statement because I didn't know its intent.