I'm not sure how the 2 situations can even be compared.
-Sasuke used genjutsu on 9 Biju with no host.
-Genjutsu was impossible in Madara's case due to 2 Perfect Jinchuriki being around.
If you replace 9 Biju with the team that faced Madara, would Sasuke have won? Depends.
Sasuke is stronger than that version of Madara, but he doesn't have the Gedo Mazo and even if he did, he doesn't have a move that is inconspicuous like Limbo in order to create an opening to seal them.
The combined Bijudama of Kurama & Gyuuki alone produced an explosion visually comparable to the one that blew off half of Sasuke's Perfect Susano'o.
A combined Bijudama from every single Biju would logically be more than double the strength of that considering that 50% Kurama=5 Biju in chakra output and Gyuuki doesn't seem much stronger than any of the other Biju if at all going by portrayal that tails=/=power except for Kurama.
A Bijudama that produces an explosion more than twice over what blew off nearly half of Sasuke's Perfect Susano'o would logically annihilate it.
The author could simply make it survive though looking haggard or have it basically destroyed with the user unharmed if he sees a Perfect Susano'o user to be above mere Biju.