What about:
datetime.now().strftime('%M:%S.%f')[:-4]
I’m not sure what you mean by “Milliseconds only 2 digits”, but this should keep it to 2 decimal places. There may be a more elegant way by manipulating the strftime format string to cut down on the precision as well — I’m not completely sure.
EDIT
If the %f modifier doesn’t work for you, you can try something like:
now=datetime.now()
string_i_want=('%02d:%02d.%d'%(now.minute,now.second,now.microsecond))[:-4]
Again, I’m assuming you just want to truncate the precision.