I have done something similar - though not exactly the same - with Win32::Process::Create. That gives you a $ProcessObj->Wait($timeout) method. However, from your description, I suspect that this will return immediately.
If Wait() does return immediately, you should be able to find an entry in the tasklist for what is running and check that periodically for the programs completion. Without being more familiar with MATLAB, I can't be any more specific.
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