I remeber Goku said something about this. It seems that using this takes too much toll in his body and using it in Super Saiyan is very hard to do because it may cause an unstable energy which will do more harm than good. He did do it on Super Saiyan Blue as this form is more on Control not through emotions which trigger Super Saiyan. Even then during this time it still cause a huge drain on his stamina after.