$id = 1; # <--- semicolon was missing
open(MYFILE,"/var/tmp/mylist.dat") or die "Cant open mylist.dat"

while (<MYFILE>) { # <--- wrong file handle fixed
      chomp;
      die "Request Id $id already present in file\n" if $_ eq $id;
}

close MYFILE;
[download]

$_, which gets assigned to by <MYFILE> in a while loop, is a scalar.
As such, it can hold a string or a number. The line is not magically split at the comma*. So, $_ just holds the entire line.

The operator eq compares its operands stringwise and returns true if both are equal. Perhaps you want to match?

      die "Request Id $id already present in file\n" if /$id/;
[download]

The match operator m// is by default bound to $_; to match against something else you need the binding operator =~:

while (my $line = <MYFILE>) {
      chomp $line;
      die "Request Id $id already present in file\n" if $line =~ /$id/
+;
}
[download]

If you really want an array and compare $id against its first element, you have to split the line into an array:

    my @array = split /,/, $_;
    die "Request Id $id already present in file\n" if $array[0] eq $id
+;
[download]

Note that split by default splits into the array @_ whose first element is $_[0] - but this usage is deprecated.

*) for magical split, look up the -a, -n, -p and -F switches, and the array @F in perlrun.