That output is being sent to STDERR rather than STDOUT. You can easily merge the two using open3 while still avoiding to spawn a needless shell.
use IPC::Open3 qw( open3 );
my @command = qw( plink -ssh -pw passwd user@host -batch exit );
open3(\*CIN, \*COUT, \*COUT, @command);
close CIN;
my $xs = <COUT>;
print "the output is :".$xs;
close COUT;
Note that the order of open3's first two argument is different than open2's.
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