They certainly did, albeit empirically.

You see, what we know now in layman's term as the 'ancient greek temple', and we usually think of the Parthenon in Athens' acropolis, wasn't a sudden architectural innovation.

The concept of the temple in ancient greece evolved through a series of different types - antae, double antae, to prostylos and eventually to the pseudoperipteros which the aforementioned Parthenon and the Hefestion on the athenian agora are prime examples of. Besides this evolution of spatial complexity and architecture, the greeks came through an evolution of construction and engineering as well, in order to be able to build larger and more complex.

First greek temples were made of wood, although we don't have any surviving examples of these, the structural concept of wooden construction has survived on into their stone offspring. The system of columns and beams as such couldn't have evolved from any other material a neolithical technological context.

As we know, wood is great in its abilities to withstand both compression and tension, whereas stone withstands compression, but can't deal with tension.

Older greek stone temples clearly show that the builders were aware of this problem, as its proportions are oversized - a good example of this is the Temple of Hera in Paestum - which clearly shows the oversized capitels on which the oversized beams are resting. As time went on, they empirically understood the concept of self-weight and limited span; so they sized the constructive elements down, trying to be more akin to the wooden temples of old, but in a new, more durable material. They eventually came to the ancient greek 'elegance' we know today, which further bloomed in the protohellenistic period, into more complex, almost manneristic pieces with greater construction spans like the Pergamon Altar.

Besides the sizes of beams and capitels, another newer practice was use of an iron core in the columns themselves - similar to the reinforced concrete, the iron taking over some of the tension and helped with the column slenderness and related issues.

While the evolution of the greek style and understanding of construction can be clearly read archaeologically, we have no written accords of a discipline of civil engineering as we know today ( de facto calculation of forces) - most of these things were invented and understood empirically, and polished through generations of builders.