Just found out the solution myself. Though I granted a point to Aidos and cjhuitt for their answers that put me on the right track and saved me valuable time. A special thanks for the link to the qmake documentation.
The first point is that I should modify the .pro file and not fiddle with the extended build arguments.
To get the content of an environment variable when qmake is processed one should use the following syntax
INCLUDEPATH += $$(MITK_INCLUDE_PATH)
Note that to get the content of an environment variable when make is processed one should use the following syntax
INCLUDEPATH += $(MITK_INCLUDE_PATH)
But this won't have the same effect if the environment variable contains multiple paths. The first form is then preferable.
Paths in the environment variable must be separated by spaces because the ; is not recognized.
If a path contain spaces, put quotes around it. Spaces appearing between the quotes will be replaced by '\ '.