You could maybe try posting data to the php app, the having the php decode what you posted and executing the mysql query and optionally returning some output. The VB.net would just "download" the php file using http(s).
You can get the POST data from requests in php with:
$post = $_POST['var_name'];
print "Any output text, including this, is what gets sent back";
print " to your vb.net app.";
Let me know if this helps!