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$| = 1;#flush the buffer
warn "Starting Program";
print "Hello World\n";
warn "Ending Program";

perl -w warn.pl
Starting Program at warn.pl line 2.
Hello World
Ending Program at warn.pl line 4.

use Log::Log4perl qw(:easy);
Log::Log4perl->easy_init($ERROR);
...
    system( 'warn.pl' );# Your favorite system call here 
};
map{ ERROR $_ } split "\n", $errors;

perl -w WarnCapture.pl
Hello World
2012/09/14 16:34:20 Starting Program at C:\Scripts\warn.pl line 2.
2012/09/14 16:34:20 Ending Program at C:\Scripts\warn.pl line 4.