Jinnah was a twelver shia.
Jinnah in his speech of September 1945 said.
"Everyone, except those who are ignorant, knows that the Quran is the general code of the Muslims. A religious, social, civil, commercial, military, judicial, criminal, penal code, it regulates everything from the ceremonies of religion to those of daily life; from the salvation of the soul to the health of the body; from the rights of all to those of each individual; from morality to crime, from punishment here to that in the life to come, and our Prophet has enjoined on us that every Musalman should possess a copy of the Quran and be his own priest. Therefore Islam is not merely confined to the spiritual tenets and doctrines or rituals and ceremonies. It is a complete code regulating the whole Muslim society, every department of life, collective[ly] and individually."
fter independence, as head of the state he had founded, Jinnah talked in the same strain. He talked of securing "liberty, fraternity and equality as enjoined upon us by Islam" (25 August 1947); of "Islamic democracy, Islamic social justice and the equality of manhood" (21 February 1948); of raising Pakistan on "sure foundations of social justice and Islamic socialism which emphasized equality and brotherhood of man" (26 March 1948); of laying "the foundations of our democracy on the basis of true Islamic ideals and principles" (14 August 1948); and "the onward march of renaissance of Islamic culture and ideals" (18 August 1947). He called upon the mammoth Lahore audience to build up "Pakistan as a bulwark of Islam", to "live up to your traditions and add to it another chapter of glory", adding, "If we take our inspiration and guidance from the Holy Quran, the final victory, I once again say, will be ours" (30 October 1947).
Now i would advise you to continuously keep guessing whether he was Shia or Sunni.