Look at the answer for question 17 in the FAQ: http://www.doxygen.nl/manual/faq.html#faq_cmdline, repeated below for convenience:
Can I configure doxygen from the command line?
Not via command line options, but doxygen can read from stdin, so you can pipe things through it. Here’s an example how to override an option in a configuration file from the command line (assuming a UNIX environment):
( cat Doxyfile ; echo "PROJECT_NUMBER=1.0" ) | doxygen -
For Windows the following would do the same:
( type Doxyfile & echo PROJECT_NUMBER=1.0 ) | doxygen.exe -
If multiple options with the same name are specified then doxygen will use the last one. To append to an existing option you can use the += operator.