As near as I can tell, Jinnah chose to stay on the sidelines until he could tell for sure which way the wind would blow, then died before he decided anything.
While I suppose it's possible Jinnah may have secretly sympathized with the heavily-outnumbered Jews' struggle against surrounding Arab states and Arab terror within - a lesser echo of the violence of Partition - Pakistan was still under the British Crown, the Brits and Zionists were engaged in active hostilities, and the struggle for a Jewish State was the least of Jinnah's concerns at the time.
The Brits didn't recognize Israel until after Jinnah died. Jinnah's successor, Liaquat Ali Khan, was more Islamist(? not sure if that's the right word) than Jinnah and championed "Muslim brotherhood" - that is, hostility to anyone fighting a Muslim anywhere for any reason - so non-recognition of Israel became set as Pakistan's official policy.
