How was higher education done before the university system? I know the university system as it is understood today dates at least as far back as the 13th century or perhaps even to the time of Charlemagne, Alcuin of York, et al., but how was higher education handled before universities? Was it by private tutoring?
As with many things the history of higher education is not well known since accounts may be scarce or missing altogether. Early evidence indicate that schools existed in Egypt where, primarily, boys would learn to read and write etc. One has to remember that such skills were not for the masses. Religiously connected schools also emerged where religious texts were handled and copied. Theological and medical teaching was also done but very little else. evidence of mathematics have been found so there were also schools, perhaps aiming at architecture, astronomy , etc. relevant for the culture. None of these has a degree at the end but was likely based on apprenticeship and mastery evaluated by the teachers. Similar evidence for teaching exists in all older cultures and seem to focus on maintaining order in the social and cultural basis for society.

There seems to be a big step when considering Greek education which was far more comprehensive than the pragmatic education earlier. In the city states of ancient Greece specialized schools emerged where teaching circled around very specific topics such as the Hippocratic school of medicine on Cos. This specialization seems to have continued with the well known Greek philosophers/scientists such as Aristotle, Plato etc. and teaching progressed in directions envisioned by these founders. In other words, there was no single systematic way for schools to teach and operate.

In the Roman world subjects were ordered in groups that we can recognize today: I grammar rhetoric, dialectic; II geometry, arithmetic, astronomy, music; III medicine, architecture. This was how the liberal arts (defined as theoretical and intellectual activities by the Greeks) were seen. The subjects have of course survived to modern times although organisation has changed. So education became more organised but the education was not open and still served a purpose for maintaining government rule. Out of the post-Roman world came the first universities as stated in the question where education became even more organized and eventually including fixed degrees.

This answer is loosely based on the excellent book: The first universities by Olaf Pedersen, Cambridge UP, 1997. I strongly recommend it!