Paladin is right - you need to set $, , not $" .

Now I'd like to suggest a few changes (improvements?) to your code. I mean, TIMTOWTDI - but this is how I might write it...

use IO::File;
use strict;
$, = "|";
my %fh; # key=filename; val=filehandle
while (<>) {
    my @record = split /\|/;
    my $word1 = shift @record;
    $fh{$word1} ||= IO::File->new("> $word1")
      or die "Error opening $word1 for writing: $!\n";
    $fh{$word1}->print( @record );
}
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What's different?

1. use strict;
2. declare all variables with my, to pass use strict;
3. Setting $, outside the loop. (Might even want to local it.)
4. Since you're using the first field for one purpose, and printing the remaining fields, shift it off the array. Then you can print the whole array (what's left).
5. Only open each output file once, and cache the filehandle in an array. To do this, need to use IO::File handles.
6. include $! in the open() error message.
7. use $_ as the loop iterator / input line. That's what it's for, and makes the code less cluttered.

Now for one further optimization: split the line directly to the desired variables:

while (<>) {
    my( $word1, @record ) = split /\|/;
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And to get really too clever:

    ( $fh{$word1} ||= IO::File->new("> $word1")
      or die "Error opening $word1 for writing: $!\n"
    )->print( @record );
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Not meant as a criticism on you code; just offered as a different perspective.

jdporter
The 6th Rule of Perl Club is -- There is no Rule #6.