I have used IPC::Open3 for this and found it worked well both on Unix and Windows. If $cmd has your command then:

use IPC::Open3;
open3("<&STDIN", \*CAPTURE, \*CAPTURE, $cmd) or die "Cannot run $cmd: 
+$!";
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Now you are reading both STDERR and STDOUT of the file from CAPTURE.

I don't know how to do this and get return codes as well though, the return of open3 is a process ID. Also note that you need to be careful with mixing filehandles. Should you try to get output while it is giving you input, programs take a while to get bored with that sort of silliness...