If you split it up so that you are only executing one SQL statement at a time, it will work fine. (using SQLite here to make it an SSCCE)

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

my $dbh = DBI->connect('dbi:SQLite:dbname=/tmp/testdb','','') or die;
my @data;

my $sth = $dbh->prepare ('select ?');
for my $arg (qw/one two three/) {
        $sth->execute ($arg);
        push @data, $sth->fetchrow_array;
}
print "$_\n" for @data;
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I expect that DBI just ignores everything after the first statement if you try to do it all at once. Another alternative would be a stored procedure but the best approach depends on what you're really trying to do.

Update: Confirmed. DBI says:

Multiple SQL statements may not be combined in a single statement handle ($sth), although some databases and drivers do support this (notably Sybase and SQL Server).