Treat "," as the end of line marker (-054).
Every third line ($. % 3 == 0),
change the trailing comma to a newline (s/,/\n/).
Print the result (-p).

perl -054pe"$.%3||s/,/\n/"
[download]

In action:

>echo a,b,c,d,e,f,g,h,i | perl -054pe"$.%3||s/,/\n/"
a,b,c
d,e,f
g,h,i
[download]

Update: As moritz points out, I assumed all the input is on one line.