talk2amulya said about changing qmake source code. you can add your own function, or modify message() to print to make file instead of console or something like this...
I don't know where exactly in your makefile your addidtional line should be but maybe modifying writeHeader() method in makefile.cpp in qmake sources (QTDIR/qmake/qmake.pro) can be enough.
P.S. or try Win32MakefileGenerator::writeStandardParts() or something like this :]
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