To make it short: yes, you can, because a civilization’s development evolves on a timeline, so this expression, which litterally means “to be early”, makes sense.

One of the cnrtl definitions of “avance” gives the following example:

Être en avance sur son temps. Le devancer par le modernisme, par le caractère d’avant-garde de ses idées.

When you use “en avance” in this context, you assume that the other party has the capability to reach the same point, only later in time. Therefore, it makes perfect sense when you are talking about civilizations developing at different speeds.

I would even say that it can be nicer to use this expression rather than “plus développés” or “supérieurs” when comparing two civilizations. This way, you just imply that one of the two has a head start, but that the other is not less capable than the other and that it will reach this level at some point.