My professor has left the university and his official email ID is no longer active
If he is still prepared to write you a reference then he will.
He can state that you were a student when he was teaching at X institution and that will be accepted.
If the admission committee feels it is necessary to contact him then they will do so.
I have sent reference letters to the Academic secretary and she printed them on letter headed paper - this was while I was on holiday in a different country and the student needed the reference quickly (comes down to planning ie 5 p's: proper planning prevents poor performance...)