Call the make command this way:
make CFLAGS=-Dvar=42
And be sure to use $(CFLAGS) in your compile command in the Makefile. As @jørgensen mentioned, putting the variable assignment after the make command will override the CFLAGS value already defined in the Makefile.
Alternatively, you could set -Dvar=42 in another variable than CFLAGS and then reuse this variable in CFLAGS to avoid completely overriding CFLAGS.