I was just playing a game with the Unfallen and couldn't figure this out either..

Then, I finally did manage it.

Guardians cannot be awoken using the system construction queue. However, the game doesn't tell you this..

You need a couple (2 or 3) scout-class ships in the System in one single fleet. They need a high enough "Curiosity level" - 2 or something like that.. Then click the "curiosities" icon - it's a square with a "?" inside it - and you'll see a similar animation to when a system is colonized except it will go and research, instantly, a curiosity in the system. This can be subterranean, anomalies, and Guardians, etc.

Once done, you should get a screen notification pop-up that a Guardian has awoken on the planet.

Yes. That's how I did it. All the planets in the system were colonized at the time, including the one with the Guardian on it.

I don't know if it works with, say, one planet colonized but it's not the one with the Guardian on it, etc.