Works for me - QMake version 2.01a. There should be no issue with that:

Qt Code:
  1. $ cat pro.pro:
  2. message($$MY_VAR | $$MY_ANOTHER_VAR)
  3. $ qmake pro.pro "CONFIG += release" "MY_VAR = hello" "MY_ANOTHER_VAR = hi"
  4. Project MESSAGE: hello | hi
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