The simplest solution, assuming unique student IDs, is so simple and somewhat idiosyncratic to Perl that my reflex is to suspect this of being a homework question... That solution is "turn your list into a hash":

my @student_info = ("001","John","002","Mary","003","Tom");
my %hash = @student_info;

say join ", ", sort keys %hash;
[download]

As a side note, you really don't want to get into the habit of sticking variable data directly into your SQL statements. Use placeholders instead.

Taking all of the above into account, your posted code becomes something like:

my @student_info = ("001","John","002","Mary","003","Tom");
my %name_hash = @student_info;

my $grade_sth = $dbh->prepare("select id from grades where id = ? and 
+grade = 'A'");

for my $student_id (sort keys %name_hash){
    $grade_sth->execute($student_id);
    my $student_name = $name_hash{$student_id};

    # do output here
}
[download]