Here is a modified version of your code that builds a hash allowing lookup either by user or smartcard id. This is assuming $b = user and $e = smartcard id (your variable names don't provide a clue). Since the arrays are 1:1, the for loop is used to generate a common index into both arrays. For your own benefit (code maintenance), please consider:

• Not using single character variable names. Some have special meaning.
• Renaming your variables to something more meaningful.
• Using lexically scoped (my) variables.

use strict;
use warnings;

my %id_lookup;

my @getuser = `dsquery user -name * -o samid -limit 1000`;

my @getcert = `dsquery usern -name * -o upn -limit 1000`;

for (0 .. scalar @getuser -1){

    my $a = $getuser[$_];
    chomp $a;
    my $b = (split (/"/, $a))[1];

    my $c = $getcert[$_];
    chomp $c;
    my $d = (split (/"/, $c))[1];
    my $e = (split (/@/, $d))[0];

    $id_lookup{$b} = $e;

    # this line adds reverse lookup, if desired
    $id_lookup{$e} = $b;
}
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