You can utilize regexes for the task. The following is a recommendation.

use warnings;
use strict;

my $user_name_regex = qr/
    ~            # match the first ~
    ([^~]+)        # capture the characters as long as it is not a ~
/x;

my $smartcard_id_regex = qr/
    ~            # match the first ~
    ([^~@]+)    # capture the characters as long as it is not a ~ or @
/x;

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

my @user_names = map {
    chomp;
    $_ =~ $user_name_regex;        # match and capture user name
    $1                            # return the capture;
} @getuser;

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

my @smartcard_ids = map {
    chomp;
    $_ =~ $smartcard_id_regex;    # match and capture smartcard id
    $1;                            # return the capture
} @getcert;
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