See PRINT Statement and Status Messages. Now put the odbc_error_handler in the same scope as the code which fetches your data and change the print statements to push the procedure output into the same array. Something like:

my @final_output;
sub err_handler {
   my ($sqlstate, $msg, $nativeerr) = @_;
   # Strip out all of the driver ID stuff
   $msg =~ s/^(\[[\w\s:]*\])+//;
   push @final_output, $msg;
   return 0;
}
$dbh->{odbc_err_handler} = \&err_handler;
my $sp_sth = $dbh->prepare('{call myproc}');
$sp_sth->execute;
do { 
   my $line; 
   while (@sp_return_data = $sp_sth->fetchrow_array()) {
      $line = join (' | ', @sp_return_data) . ".\n";
      push @final_output, $line;
      }
} while ($sp_sth->{odbc_more_results});
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