Rather than interpolating values directly into your SQL, you should probably get into the habit of using placeholders. In addition to improving security, it handles escaping for you. It also lets you only prepare your statement once, and use it multiple times. By moving that and your connect statement outside the loop, you'll likely find my rewrite runs substantially faster.

#!/usr/bin/perl
use DBI;
use strict;


  my @date1 = ('2013-08-01 00:00:00.000','2013-08-02 00:00:00.000');
  my @date2 = ('2013-08-02 00:00:00.000','2013-08-03 00:00:00.000');
  
my $dbh = DBI-> connect('dbi:ODBC:DSN=TEST-DB1;UID=SA;PWD=pass') or di
+e "CONNECT ERROR! :: $DBI::err $DBI::errstr $DBI::state $!\n"

my $sql2 = <<EOSQL;
SELECT Login_ID, AuditChrt_TimeStamp, Patient_ID
FROM TopsData.dbo.AUDT_AuditChrt
WHERE master.dbo.fn_sqlvarbasetostr(AuditChrt_TimeStamp) >= ?    
AND master.dbo.fn_sqlvarbasetostr(AuditChrt_TimeStamp) <= ?
EOSQL
my $sth = $dbh->prepare($sql2);

foreach my $i (0 .. @date1 - 1) {
    $sth->execute($date1[$i], $date2[$i]);
    my @row;
    while (@row = $sth->fetchrow_array) {  # retrieve one row at a tim
+e
        print join(", ", @row), "\n";
    }
} 

END {
    $dbh->disconnect if $dbh;
}
[download]

Other changes I made:

• I used a heredoc (Quote and Quote like Operators in perlop) to separate the SQL from the Perl code; IMHO, it makes things more legible

• I swapped to a foreach loop, since that structure is less bug prone than C-style loops -- fewer moving parts.

• I moved the disconnect to an END block (with conditional) so that no matter how your code exits, you won't get that pesky Issuing rollback warning.

Update: Corrected copy&paste bug, as per McA's comment below. I concur that an AoA is a better data structure here, but wanted to not get too far too fast...

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