Quick and dirty, check if you're at the end of file:

use warnings;
use strict;

open my $fh, '<', 'file.txt'
  or die "can't open the damned file!: $!";

while (<$fh>){
    chomp;

    if (! eof){
        print "$_,\n";
    }
    else {
        print "$_\n";
    }
}
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Where 'file.txt' contains:

one
two
three
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Output:

one,
two,
three
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